nservant HiC-Pro issues

nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

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proposed chimeric reads

#661 ejc043 opened 2 days ago
0
mergeSAM.py error

#660 WanghcPKU opened 3 days ago
4
mergeSAM.py error

#659 WanghcPKU opened 3 days ago
0
mergeSAM.py error

#658 WanghcPKU opened 3 days ago
0
About the read pairing.

#657 GleeenSIBS opened 1 week ago
0
Error in Hi-C Pro non processing all the files

#656 robertferr opened 1 week ago
1
Error in reads alignment

#655 robertferr closed 2 weeks ago
4
About Arima Hi-C Kit restiction.

#654 GleeenSIBS opened 2 weeks ago
0
It seems that all the input files for mergeBAM.py are R2.

#653 yangqihang1230 opened 4 weeks ago
0
Allelic analysis HiC-Pro G2 genome not mapping

#652 luckysardar opened 1 month ago
4
How can I generate a .hic contact matrix at the fragment level using Micro-C data?

#651 hanshanmengqi opened 1 month ago
0
how to set temporary home directory

#650 ahmedabbas811 opened 2 months ago
1
mergeSAM.log error

#649 hcsun1 opened 2 months ago
2
what is the Dumped_Pairs files about

#648 Hanjiangna opened 2 months ago
4
Valid_interaction_pairs is 0

#647 Hanjiangna closed 2 months ago
1
HiC-Pro_3.1.0 failed to trim 3' end of the unmapped reads?

#646 ddzhang3 opened 2 months ago
1
sbatch: error: Invalid --time specification

#645 Hanjiangna closed 2 months ago
0
bowtie2-align died with signal 7 (BUS)

#644 mengying0714 opened 2 months ago
2
Automatically ends HiC-Pro without any prompt

#643 XuanZhang-Black opened 3 months ago
2
Error in Hicpro2higlass

#642 ratheraarif opened 3 months ago
0
Error after installation using conda

#641 aplearnercc opened 3 months ago
1
When I run the last step of HiC-Pro, “ice_norm”, I get the error：“binary operator expected ”

#640 kuangzhuoran closed 3 months ago
1
I would like to understand if the software supports specifying multiple values for LIGATION_SITE in a single config file

#639 tangyueting closed 4 months ago
1
HiC-Pro: Error in Quality Checks

#638 AnushkaChaturvedi opened 4 months ago
1
Error in HiC-Pro 3.1.0 step1

#637 AnushkaChaturvedi closed 4 months ago
3
How to delete duplicate pairs when using hicpro at high resolution?

#636 xingql983 opened 5 months ago
1
How do I set up and run the single-ended reads when I am using them?

#635 wangguiqian closed 2 months ago
1
bowtie install errors

#634 elirahbar opened 5 months ago
0
"Forward and reverse reads not paired. Check that BAM files have the same read names and are sorted."

#633 panapapa14 opened 6 months ago
5
Process data type

#632 Blosers closed 6 months ago
2
Restriction fragments difference generated from HiC-Pro (digest_genome.py) and Juicer for Arima

#631 vikaskumar1019 closed 6 months ago
1
Polyploidy

#630 Rhia15 closed 6 months ago
1
line:303

#629 Blosers opened 7 months ago
0
Update extract_snps.py

#628 EmmanuelCzt opened 7 months ago
0
make: *** [bowtie_pairing] Error 1

#627 wangguiqian opened 8 months ago
0
Low Read Alignment in Initial Bowtie Step

#626 IzaakH-A1 opened 8 months ago
1
hicpro2juicebox.sh not work for nextflow pipe https://github.com/nservant/nf-core-hic/tree/master

#625 XuewenWangUGA opened 8 months ago
0
Bowtie2 alignment step1 ... Logs: logs/Control1/mapping_step1.log

#624 Woogle90 closed 8 months ago
1
contact map in complete format instead of upper

#623 usernicai opened 8 months ago
0
HiC-Pro for ChIA-PET data analysis

#622 Huang-XN opened 9 months ago
0
From allvalidpairs to mcool

#621 ratheraarif opened 9 months ago
0
HiC-Pro not reporting fragment size in allValidPairs file

#620 sunilnahata opened 9 months ago
0
converting allvalidpairs to pairs

#619 ratheraarif opened 9 months ago
13
hicpro2juicebox.sh: allValidPairs.pre_juicebox_sorted does not exist or does not contain any reads

#618 TheRaspberryFox opened 10 months ago
1
hicpro2juicebox.sh: line 152: java: command not found

#617 qqyanyang closed 10 months ago
1
Can multiple nodes be set for parallel processing in HiC-Pro (Torque)?

#616 YCMaCY closed 10 months ago
2
gensub: third argument treated as 1

#615 KarimKoleilat opened 10 months ago
3
merge allValidPairs and convert to .hic

#614 mw18f closed 10 months ago
4
Small fix to replace egrep with grep -E and silence warning messages

#613 mtekman closed 10 months ago
0
how to index bam files after sorting by reads name ?

#612 wu123tj opened 10 months ago
1