nservant HiC-Pro issues

nservant / HiC-Pro

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

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How to delete duplicate pairs when using hicpro at high resolution?

#636 xingql983 opened 2 weeks ago
0
How do I set up and run the single-ended reads when I am using them?

#635 wangguiqian opened 4 weeks ago
0
bowtie install errors

#634 elirahbar opened 1 month ago
0
"Forward and reverse reads not paired. Check that BAM files have the same read names and are sorted."

#633 panapapa14 opened 1 month ago
3
Process data type

#632 Blosers closed 1 month ago
2
Restriction fragments difference generated from HiC-Pro (digest_genome.py) and Juicer for Arima

#631 vikaskumar1019 closed 1 month ago
1
Polyploidy

#630 Rhia15 closed 1 month ago
1
line:303

#629 Blosers opened 2 months ago
0
Update extract_snps.py

#628 EmmanuelCzt opened 3 months ago
0
make: *** [bowtie_pairing] Error 1

#627 wangguiqian opened 3 months ago
0
Low Read Alignment in Initial Bowtie Step

#626 IzaakH-A1 opened 3 months ago
1
hicpro2juicebox.sh not work for nextflow pipe https://github.com/nservant/nf-core-hic/tree/master

#625 XuewenWangUGA opened 3 months ago
0
Bowtie2 alignment step1 ... Logs: logs/Control1/mapping_step1.log

#624 Woogle90 closed 3 months ago
1
contact map in complete format instead of upper

#623 usernicai opened 4 months ago
0
HiC-Pro for ChIA-PET data analysis

#622 Huang-XN opened 4 months ago
0
From allvalidpairs to mcool

#621 ratheraarif opened 4 months ago
0
HiC-Pro not reporting fragment size in allValidPairs file

#620 sunilnahata opened 4 months ago
0
converting allvalidpairs to pairs

#619 ratheraarif opened 5 months ago
13
hicpro2juicebox.sh: allValidPairs.pre_juicebox_sorted does not exist or does not contain any reads

#618 TheRaspberryFox opened 5 months ago
1
hicpro2juicebox.sh: line 152: java: command not found

#617 qqyanyang closed 5 months ago
1
Can multiple nodes be set for parallel processing in HiC-Pro (Torque)?

#616 YCMaCY closed 5 months ago
2
gensub: third argument treated as 1

#615 KarimKoleilat opened 5 months ago
3
merge allValidPairs and convert to .hic

#614 mw18f closed 5 months ago
1
Small fix to replace egrep with grep -E and silence warning messages

#613 mtekman closed 5 months ago
0
how to index bam files after sorting by reads name ?

#612 wu123tj opened 5 months ago
1
HiC-Pro --help

#611 ryao-mdanderson closed 6 months ago
2
juicer jar tools in hicpro2juicebox.sh

#610 usernicai closed 5 months ago
1
Can I use hic-pro for Hi-C 3.0 ?

#609 hanshanmengqi opened 6 months ago
1
Bowtie global error

#608 CarolWuuu closed 5 months ago
1
test dataset link not working HiCPro_testdata.tar.gz

#607 dksenthil closed 5 months ago
2
reformat print line to get rid off unwanted spaces

#606 WardDeb opened 6 months ago
2
Exit: Read pairs extensions not defined

#605 usernicai closed 6 months ago
4
Bowtie2 alignment step1 ... make: /student2/software/hicpro/scripts/bowtie_wrap.sh: Command not found make: *** [/student2/software/hicpro/HiC-Pro-3.1.0/bin/../scripts//Makefile:88: bowtie_global] Error 127

#604 lixinrong0118 closed 5 months ago
0
make: *** No targets. Stop.

#603 AlcaArctica opened 7 months ago
3
extra \n in hicpro2fithic.py

#602 ay-lab opened 7 months ago
0
Is there any solution about using DdeI in HiC-PRO?

#601 khsjh opened 7 months ago
1
allmapstat_r1 <- list.files(path=bwtDir, pattern=paste0("^[[:print:]]*",r1tag,"[[:print:]]*\\.mapstat$"), full.names=TRUE)

#600 Oksanak22 opened 8 months ago
0
Make: *** [HiC-Pro_3.1.0/bin/../scripts//Makefile:181: hic_qc] Error 1

#599 Oksanak22 opened 8 months ago
0
Can Allele specific mapping handle polyploids?

#598 Adamtaranto opened 8 months ago
1
make install error

#597 IIrfan57 closed 8 months ago
1
Exit: Error: Directory Hierarchy of rawdata '/home/ug1287/workspace/Hicdata_analysisi/rawdata/HJB/' is not correct. No '.fastq(.gz)' files detected

#596 15132522078 opened 8 months ago
1
make configure error - python libraries

#595 hwamu opened 9 months ago
1
Makefile:181:hic_qc error1 / allValidPairs file is empty

#594 yuntan1992 opened 9 months ago
2
makefile

#593 twdawd opened 9 months ago
0
Installation error

#592 ratheraarif opened 9 months ago
0
Step2 Error: recipe commences before first target

#591 Elliott77 opened 9 months ago
0
Conversion of validpairs to .HIC or hicpro format

#590 gk1610 opened 9 months ago
0
Unable to download test dataset

#589 varunkas closed 6 months ago
2
Update the shebang line of ice

#588 qiyubio closed 5 months ago
0
Update make_viewpoints.py to convert exclusionSize to int

#587 qiyubio closed 5 months ago
0