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xie186 / ViewBS

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
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MethHeatmap and MethGeno Problems #47

Closed hanahm1 closed 3 years ago

hanahm1 commented 4 years ago

Hi all,

I am having two issues that is probably associated with my not being familiar with ViewBS.

First: MethGeno- I can successfully run MethGeno with CHH and CHG contexts. When I ask for CpG/CG context, the output graph puts all the samples at a methylation level of 1. I can't seem to figure out why. See code below:

./ViewBS MethGeno --genomeLength /lab_data/hansen_lab/hanahm1/bosTau9_genome/bosTau9.fa.fai --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F272_C.bis_rep.cov.CX_report.txt.gz,C272 --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F250_C.bis_rep.cov.CX_report.txt.gz,C250 --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F268_C.bis_rep.cov.CX_report.txt.gz,C268 --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F278_C.bis_rep.cov.CX_report.txt.gz,C278 --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F307_PI.bis_rep.cov.CX_report.txt.gz,PI307 --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F308_PI.bis_rep.cov.CX_report.txt.gz,PI308 --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F842_PI.bis_rep.cov.CX_report.txt.gz,PI842 --maxChromNum 3000 --outdir /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/test_plots/ --prefix MethGeno --context CG Second: MethHeatmap- I get the following error when running MethHeatmap

'Output directory is: /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/HeatMap Output prefix: CHG-Hyper-HeatMap Start calculate methylation information for target context CHG Error in read.table(cpg, header = T) : more columns than column names Execution halted Meth::Heatmap=HASH(0x55a968109380): Useage: R --vanilla --slave --input <> --height --width --height2 --width2 --random_region --output1 --output2 < trans_DMS_heatmap.R /home/hanahm1/miniconda3/envs/ViewBS/lib/R/bin/exec/R --slave --no-restore --file=/home/hanahm1/ViewBS/ViewBS-0.1.9/lib/Meth/Heatmap.R --args --input /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/HeatMap/CHG-Hyper-HeatMap_MethHeatmap_CHG.txt --output1 /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/HeatMap/CHG-Hyper-HeatMap_MethHeatmap_CHG.pdf --output2 /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/HeatMap/CHG-Hyper-HeatMap_MethHist_CHG.pdf --cluster_cols FALSE --cluster_rows TRUE --height 10 --width 10 --height2 10 --width2 10 --random_region 2000 FALSE TRUE

Running time: 1 wallclock secs ( 0.44 usr 0.05 sys + 1.37 cusr 7.78 csys = 9.64 CPU)'

I'm certain it has to do with the reference table which can be seen below

'"chr13" 59054354 59054354 "NR_031115.1" "chr16" 41909887 41909887 "XM_024976558.1" "chr2" 131185958 131185958 "XM_015460007.2" "chr25" 25228240 25228240 "XM_024985093.1" "chr25" 27328872 27328872 "NM_001039957.1" "chr25" 41206122 41206122 "NM_001206549.1" "chr26" 23398931 23398931 "NM_174304.2" "chr26" 39112822 39112822 "XM_024986064.1" "chr27" 40512069 40512069 "XM_024986389.1" "chr27" 40512073 40512073 "XM_024986389.1.a" "chr27" 40512150 40512150 "XM_024986389.1.b" ' I have tried with and without column headers. The code run is below:

'./ViewBS MethHeatmap --region /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/DMRs/CHG_hyper3.txt --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F272_C.bis_rep.cov.CX_report.txt.gz,C272 --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F250_C.bis_rep.cov.CX_report.txt.gz,C250 --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F268_C.bis_rep.cov.CX_report.txt.gz,C268 --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F278_C.bis_rep.cov.CX_report.txt.gz,C278 --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F307_PI.bis_rep.cov.CX_report.txt.gz,PI307 --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F308_PI.bis_rep.cov.CX_report.txt.gz,PI308 --sample /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/Bismark_output/cytosine_reports/F842_PI.bis_rep.cov.CX_report.txt.gz,PI842 --outdir /lab_data/hansen_lab/hanahm1/Methyl-Seq/Methyl-Seq_Data/HeatMap/ --prefix CHG-Hyper-HeatMap --context CHG '

Thank you so much for your help.

Best,

Hanah

xie186 commented 4 years ago

Could you please attached a piece of the file with CG methylation information? You can send to my email at xie186@purdue.edu if you want to keep it confidential. Thanks.