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ay-lab / dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets
MIT License
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Update piped calls to 'sort -k 1,1' in dchicf.r to 'sort -k1,1V,' which prevents bedtools chromosome-order (and subsequent) errors when running 'dchicf.r --pcatype select' #80

Closed kalavattam closed 7 months ago

kalavattam commented 7 months ago

Hi @ay-lab,

Thank you so much for making and maintaining this tool. I'm using the most recent dcHiC version 2. I encountered a bug in which, when running dchicf.r --pcatype select, the resulting GCpt.bedGraph file was sorted in "chromosome string"/lexicographic order rather than "chromosome numerical"/natural order:

Observed and expected outfile chromosome orders Observed outfile chromosome order (chromosome string/lexicographic order) ```txt cat Homo_sapiens.GRCh38.110.GCpt.bedGraph | cut -f1 | uniq 1 10 11 12 13 14 15 16 17 18 19 2 20 21 22 3 4 5 6 7 8 9 X ``` Expected outfile chromosome order (chromosome numerical/natural order) ```txt cat Homo_sapiens.GRCh38.110.GCpt.bedGraph | cut -f1 | uniq 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X ```


This resulted in the following errors:

Error text, etc. ```txt ❯ if ${submit_job}; then > Rscript "${dir_dcHiC}/dchicf.r" \ > --file "${infile}" \ > --pcatype select \ > --dirovwt T \ > --genome "${name_genome}" \ > --gfolder "${dir_base}/${dir_proj}/${name_genome}_${res}_goldenpathData" > fi Running /home/kalavatt/miniconda3/envs/dcHiC_env/bin/bedtools makewindows -g /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_40000_goldenpathData/Homo_sapiens.GRCh38.110.chrom.sizes -w 40000 > /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_40000_goldenpathData/Homo_sapiens.GRCh38.110.binned.bed Running /home/kalavatt/miniconda3/envs/dcHiC_env/bin/bedtools nuc -fi /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_40000_goldenpathData/Homo_sapiens.GRCh38.110.fa -bed /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_40000_goldenpathData/Homo_sapiens.GRCh38.110.binned.bed |grep -v "#" |awk -v OFS='\t' '{print $1,$2,$3,$5}' |grep -v "alt" |grep -v "random" |sort -k 1,1 -k2,2n > /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_40000_goldenpathData/Homo_sapiens.GRCh38.110.GCpt.bedGraph Running /home/kalavatt/miniconda3/envs/dcHiC_env/bin/bedtools map -a /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_40000_goldenpathData/Homo_sapiens.GRCh38.110.GCpt.bedGraph -b /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_40000_goldenpathData/Homo_sapiens.GRCh38.110.tss.bed -c 1 -o count -null 0 > /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_40000_goldenpathData/Homo_sapiens.GRCh38.110.GCpt.tss.bedGraph ERROR: chromomsome sort ordering for file /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_40000_goldenpathData/Homo_sapiens.GRCh38.110.tss.bed is inconsistent with other files. Record was: 10 20930 20931 ENSG00000260370 0 - Running intra 1 in D14_no2_40000 sample Running intra 1 in D14_no7_40000 sample Running intra 2 in D14_no2_40000 sample Running intra 2 in D14_no7_40000 sample Running intra 3 in D14_no2_40000 sample Running intra 3 in D14_no7_40000 sample Running intra 4 in D14_no2_40000 sample Running intra 4 in D14_no7_40000 sample Running intra 5 in D14_no2_40000 sample Running intra 5 in D14_no7_40000 sample Running intra 6 in D14_no2_40000 sample Running intra 6 in D14_no7_40000 sample Running intra 7 in D14_no2_40000 sample Running intra 7 in D14_no7_40000 sample Running intra 8 in D14_no2_40000 sample Running intra 8 in D14_no7_40000 sample Running intra 9 in D14_no2_40000 sample Running intra 9 in D14_no7_40000 sample Error in hclust(as.dist(round(1 - cor(pc.mat), 4))) : NA/NaN/Inf in foreign function call (arg 10) Calls: pcselect -> pcselectioncore -> hclust Execution halted ```


How I am calling dcHiC thus far:

Calls to dcHiC ```bash # Step 1 Rscript "${dir_dcHiC}/dchicf.r" \ --file "${infile}" \ --pcatype cis \ --dirovwt T \ --cthread $(( threads )) \ --pthread $(( threads )) # Step 2 Rscript "${dir_dcHiC}/dchicf.r" \ --file "${infile}" \ --pcatype select \ --dirovwt T \ --genome "${name_genome}" \ --gfolder "${dir_base}/${dir_proj}/${name_genome}_${res}_goldenpathData" ```


Solution: The issue arises due to the default sorting behavior of the sort command, which doesn't handle numeric sorting of chromosomes in the natural order. One solution is to modify the relevant sort command within the dcHiC script to use the --version-sort (-V) option. This option enables natural sorting of numbers, ensuring chromosomes are sorted in the correct numerical order rather than lexicographically. This change corrects the chromosome order in the output files and resolve the discrepancies encountered during processing.

I believe -V is available in both GNU and BSD versions of sort. I've only tested this with GNU versions.

After the fix:

Messages following the fix ```txt ❯ if ${submit_job}; then > Rscript "${dir_dcHiC}/dchicf.r" \ > --file "${infile}" \ > --pcatype select \ > --dirovwt T \ > --genome "${name_genome}" \ > --gfolder "${dir_base}/${dir_proj}/${name_genome}_${res}_goldenpathData" > fi Running /home/kalavatt/miniconda3/envs/dcHiC_env/bin/bedtools makewindows -g /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.chrom.sizes -w 250000 > /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.binned.bed Running /home/kalavatt/miniconda3/envs/dcHiC_env/bin/bedtools nuc -fi /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.fa -bed /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.binned.bed |grep -v "#" |awk -v OFS='\t' '{print $1,$2,$3,$5}' |grep -v "alt" |grep -v "random" |sort -k1,1V -k2,2n > /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.GCpt.bedGraph Running /home/kalavatt/miniconda3/envs/dcHiC_env/bin/bedtools makewindows -g /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.chrom.sizes -w 250000 > /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.binned.bed Running /home/kalavatt/miniconda3/envs/dcHiC_env/bin/bedtools nuc -fi /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.fa -bed /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.binned.bed |grep -v "#" |awk -v OFS='\t' '{print $1,$2,$3,$5}' |grep -v "alt" |grep -v "random" |sort -k1,1V -k2,2n > /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.GCpt.bedGraph Running /home/kalavatt/miniconda3/envs/dcHiC_env/bin/bedtools map -a /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.GCpt.bedGraph -b /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.tss.bed -c 1 -o count -null 0 > /fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/results/2023-1018_work_Hi-C_align-process/Homo_sapiens.GRCh38.110_250000_goldenpathData/Homo_sapiens.GRCh38.110.GCpt.tss.bedGraph Running intra 1 in D14_no2_250000 sample Running intra 1 in D14_no7_250000 sample Running intra 2 in D14_no2_250000 sample Running intra 2 in D14_no7_250000 sample Running intra 3 in D14_no2_250000 sample Running intra 3 in D14_no7_250000 sample Running intra 4 in D14_no2_250000 sample Running intra 4 in D14_no7_250000 sample Running intra 5 in D14_no2_250000 sample Running intra 5 in D14_no7_250000 sample Running intra 6 in D14_no2_250000 sample Running intra 6 in D14_no7_250000 sample Running intra 7 in D14_no2_250000 sample Running intra 7 in D14_no7_250000 sample Running intra 8 in D14_no2_250000 sample Running intra 8 in D14_no7_250000 sample Running intra 9 in D14_no2_250000 sample Running intra 9 in D14_no7_250000 sample Running intra 10 in D14_no2_250000 sample Running intra 10 in D14_no7_250000 sample Running intra 11 in D14_no2_250000 sample Running intra 11 in D14_no7_250000 sample Running intra 12 in D14_no2_250000 sample Running intra 12 in D14_no7_250000 sample Running intra 13 in D14_no2_250000 sample Running intra 13 in D14_no7_250000 sample Running intra 14 in D14_no2_250000 sample Running intra 14 in D14_no7_250000 sample Running intra 15 in D14_no2_250000 sample Running intra 15 in D14_no7_250000 sample Running intra 16 in D14_no2_250000 sample Running intra 16 in D14_no7_250000 sample Running intra 17 in D14_no2_250000 sample Running intra 17 in D14_no7_250000 sample Running intra 18 in D14_no2_250000 sample Running intra 18 in D14_no7_250000 sample Running intra 19 in D14_no2_250000 sample Running intra 19 in D14_no7_250000 sample Running intra 20 in D14_no2_250000 sample Running intra 20 in D14_no7_250000 sample Running intra 21 in D14_no2_250000 sample Running intra 21 in D14_no7_250000 sample Running intra 22 in D14_no2_250000 sample Running intra 22 in D14_no7_250000 sample Running intra X in D14_no2_250000 sample Running intra X in D14_no7_250000 sample Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/1.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/1.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/1.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/1.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/2.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/2.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/2.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/2.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/3.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/3.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/3.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/3.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/4.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/4.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/4.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/4.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/5.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/5.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/5.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/5.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/6.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/6.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/6.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/6.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/7.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/7.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/7.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/7.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/8.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/8.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/8.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/8.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/9.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/9.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/9.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/9.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/10.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/10.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/10.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/10.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/11.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/11.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/11.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/11.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/12.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/12.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/12.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/12.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/13.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/13.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/13.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/13.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/14.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/14.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/14.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/14.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/15.PC2.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/15.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/15.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/15.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/16.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/16.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/16.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/16.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/17.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/17.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/17.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/17.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/18.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/18.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/18.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/18.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/19.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/19.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/19.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/19.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/20.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/20.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/20.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/20.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/21.PC2.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/21.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/21.PC2.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/21.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/22.PC1.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/22.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/22.PC1.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/22.pc.bedGraph Running cp D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/X.PC2.bedGraph D14_no2_250000_pca/intra_pca/D14_no2_250000_mat/X.pc.bedGraph Running cp D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/X.PC2.bedGraph D14_no7_250000_pca/intra_pca/D14_no7_250000_mat/X.pc.bedGraph Running intra 1 in Tx-ctrl_no2_250000 sample Running intra 1 in Tx-ctrl_no7_250000 sample Running intra 2 in Tx-ctrl_no2_250000 sample Running intra 2 in Tx-ctrl_no7_250000 sample Running intra 3 in Tx-ctrl_no2_250000 sample Running intra 3 in Tx-ctrl_no7_250000 sample Running intra 4 in Tx-ctrl_no2_250000 sample Running intra 4 in Tx-ctrl_no7_250000 sample Running intra 5 in Tx-ctrl_no2_250000 sample Running intra 5 in Tx-ctrl_no7_250000 sample Running intra 6 in Tx-ctrl_no2_250000 sample Running intra 6 in Tx-ctrl_no7_250000 sample Running intra 7 in Tx-ctrl_no2_250000 sample Running intra 7 in Tx-ctrl_no7_250000 sample Running intra 8 in Tx-ctrl_no2_250000 sample Running intra 8 in Tx-ctrl_no7_250000 sample Running intra 9 in Tx-ctrl_no2_250000 sample Running intra 9 in Tx-ctrl_no7_250000 sample Running intra 10 in Tx-ctrl_no2_250000 sample Running intra 10 in Tx-ctrl_no7_250000 sample Running intra 11 in Tx-ctrl_no2_250000 sample Running intra 11 in Tx-ctrl_no7_250000 sample Running intra 12 in Tx-ctrl_no2_250000 sample Running intra 12 in Tx-ctrl_no7_250000 sample Running intra 13 in Tx-ctrl_no2_250000 sample Running intra 13 in Tx-ctrl_no7_250000 sample Running intra 14 in Tx-ctrl_no2_250000 sample Running intra 14 in Tx-ctrl_no7_250000 sample Running intra 15 in Tx-ctrl_no2_250000 sample Running intra 15 in Tx-ctrl_no7_250000 sample Running intra 16 in Tx-ctrl_no2_250000 sample Running intra 16 in Tx-ctrl_no7_250000 sample Running intra 17 in Tx-ctrl_no2_250000 sample Running intra 17 in Tx-ctrl_no7_250000 sample Running intra 18 in Tx-ctrl_no2_250000 sample Running intra 18 in Tx-ctrl_no7_250000 sample Running intra 19 in Tx-ctrl_no2_250000 sample Running intra 19 in Tx-ctrl_no7_250000 sample Running intra 20 in Tx-ctrl_no2_250000 sample Running intra 20 in Tx-ctrl_no7_250000 sample Running intra 21 in Tx-ctrl_no2_250000 sample Running intra 21 in Tx-ctrl_no7_250000 sample Running intra 22 in Tx-ctrl_no2_250000 sample Running intra 22 in Tx-ctrl_no7_250000 sample Running intra X in Tx-ctrl_no2_250000 sample Running intra X in Tx-ctrl_no7_250000 sample Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/1.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/1.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/1.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/1.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/2.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/2.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/2.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/2.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/3.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/3.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/3.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/3.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/4.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/4.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/4.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/4.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/5.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/5.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/5.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/5.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/6.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/6.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/6.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/6.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/7.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/7.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/7.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/7.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/8.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/8.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/8.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/8.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/9.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/9.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/9.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/9.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/10.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/10.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/10.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/10.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/11.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/11.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/11.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/11.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/12.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/12.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/12.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/12.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/13.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/13.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/13.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/13.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/14.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/14.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/14.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/14.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/15.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/15.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/15.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/15.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/16.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/16.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/16.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/16.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/17.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/17.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/17.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/17.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/18.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/18.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/18.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/18.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/19.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/19.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/19.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/19.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/20.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/20.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/20.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/20.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/21.PC2.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/21.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/21.PC2.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/21.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/22.PC1.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/22.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/22.PC1.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/22.pc.bedGraph Running cp Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/X.PC2.bedGraph Tx-ctrl_no2_250000_pca/intra_pca/Tx-ctrl_no2_250000_mat/X.pc.bedGraph Running cp Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/X.PC2.bedGraph Tx-ctrl_no7_250000_pca/intra_pca/Tx-ctrl_no7_250000_mat/X.pc.bedGraph Running intra 1 in Tx-MM_no2_250000 sample Running intra 1 in Tx-MM_no7_250000 sample Running intra 2 in Tx-MM_no2_250000 sample Running intra 2 in Tx-MM_no7_250000 sample Running intra 3 in Tx-MM_no2_250000 sample Running intra 3 in Tx-MM_no7_250000 sample Running intra 4 in Tx-MM_no2_250000 sample Running intra 4 in Tx-MM_no7_250000 sample Running intra 5 in Tx-MM_no2_250000 sample Running intra 5 in Tx-MM_no7_250000 sample Running intra 6 in Tx-MM_no2_250000 sample Running intra 6 in Tx-MM_no7_250000 sample Running intra 7 in Tx-MM_no2_250000 sample Running intra 7 in Tx-MM_no7_250000 sample Running intra 8 in Tx-MM_no2_250000 sample Running intra 8 in Tx-MM_no7_250000 sample Running intra 9 in Tx-MM_no2_250000 sample Running intra 9 in Tx-MM_no7_250000 sample Running intra 10 in Tx-MM_no2_250000 sample Running intra 10 in Tx-MM_no7_250000 sample Running intra 11 in Tx-MM_no2_250000 sample Running intra 11 in Tx-MM_no7_250000 sample Running intra 12 in Tx-MM_no2_250000 sample Running intra 12 in Tx-MM_no7_250000 sample Running intra 13 in Tx-MM_no2_250000 sample Running intra 13 in Tx-MM_no7_250000 sample Running intra 14 in Tx-MM_no2_250000 sample Running intra 14 in Tx-MM_no7_250000 sample Running intra 15 in Tx-MM_no2_250000 sample Running intra 15 in Tx-MM_no7_250000 sample Running intra 16 in Tx-MM_no2_250000 sample Running intra 16 in Tx-MM_no7_250000 sample Running intra 17 in Tx-MM_no2_250000 sample Running intra 17 in Tx-MM_no7_250000 sample Running intra 18 in Tx-MM_no2_250000 sample Running intra 18 in Tx-MM_no7_250000 sample Running intra 19 in Tx-MM_no2_250000 sample Running intra 19 in Tx-MM_no7_250000 sample Running intra 20 in Tx-MM_no2_250000 sample Running intra 20 in Tx-MM_no7_250000 sample Running intra 21 in Tx-MM_no2_250000 sample Running intra 21 in Tx-MM_no7_250000 sample Running intra 22 in Tx-MM_no2_250000 sample Running intra 22 in Tx-MM_no7_250000 sample Running intra X in Tx-MM_no2_250000 sample Running intra X in Tx-MM_no7_250000 sample Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/1.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/1.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/1.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/1.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/2.PC2.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/2.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/2.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/2.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/3.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/3.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/3.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/3.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/4.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/4.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/4.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/4.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/5.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/5.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/5.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/5.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/6.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/6.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/6.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/6.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/7.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/7.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/7.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/7.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/8.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/8.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/8.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/8.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/9.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/9.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/9.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/9.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/10.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/10.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/10.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/10.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/11.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/11.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/11.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/11.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/12.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/12.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/12.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/12.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/13.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/13.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/13.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/13.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/14.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/14.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/14.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/14.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/15.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/15.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/15.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/15.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/16.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/16.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/16.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/16.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/17.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/17.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/17.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/17.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/18.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/18.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/18.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/18.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/19.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/19.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/19.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/19.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/20.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/20.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/20.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/20.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/21.PC2.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/21.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/21.PC2.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/21.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/22.PC1.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/22.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/22.PC1.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/22.pc.bedGraph Running cp Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/X.PC2.bedGraph Tx-MM_no2_250000_pca/intra_pca/Tx-MM_no2_250000_mat/X.pc.bedGraph Running cp Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/X.PC2.bedGraph Tx-MM_no7_250000_pca/intra_pca/Tx-MM_no7_250000_mat/X.pc.bedGraph ❯ echo $? 0 ```


ay-lab commented 7 months ago

Hi, Thanks for the suggestion. However, I didn't test dcHiC on bedfiles using numeric chromosome names and I am almost sure that it will have some downstream effect on some functions. Is it must for you to use numeric chromosome names?

kalavattam commented 7 months ago

Thank you for your response.

I understand your concern regarding the testing of dcHiC with numeric chromosome names and the potential downstream effects on some functions. My data preparation was based on Ensembl files, which use numeric chromosome names. However, if appending "chr" to the chromosome names will align better with dcHiC's expected inputs and avoid any issues, I am more than willing to make that adjustment.

Additionally, it might be beneficial for users if the documentation explicitly states that chromosome names are expected to be prefixed with "chr." (Apologies if this note exists and I've missed it.) This clarification could help others who are using similar data sources.

Thank you once again for your prompt response and for maintaining dcHiC!

ay-lab commented 7 months ago

Hi,

It was not explicitly mentioned, but now it has. Thanks a lot for the suggestion.