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StevenWingett / HiCUP

Hi-C data processing pipeline
GNU Lesser General Public License v3.0
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Hicup capture script not working #59

Closed aturocks closed 3 years ago

aturocks commented 3 years ago

Hello,

I am working through the tutorial in the Nature Protocols paper "Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools" (https://www.nature.com/articles/s41596-021-00567-5). I have downloaded their downsampled test data (the MyLa cell line) from https://osf.io/kt67f/ and have run the HiCUP pipeline successfully. However, when I run the hicup_capture step

perl Misc/hicup_capture --baits designDir/HindIII_GWAS_baits.txt MyLa_rep1_CHiC_DS20M_R1_2.filt.bam

I get an empty object for the captured BAM file. The capture_summary.txt is attached below. Do you know why this is happening? I am using the same bait file as in the paper (from https://osf.io/sx7fu/), and am also attaching it below. I have also aligned everything to hg19 coordinates (as in the paper).

capture_summary.txt HindIII_GWAS_baits.txt

StevenWingett commented 3 years ago

Hi,

Thanks for your message. Mapping 0 di-tags is very unlikely, even for a non-capture Hi-C library.

I was just wondering, are the chromosome names in the genome file (FASTA file used to build Bowtie2 indices) exactly the same as in the baits file? Often an additional "chr" causes the problem. The baits file names chromosomes as 1, 2, 3,... Does your genome file name them as chr1, chr2, chr3? If so, please adjust one of these files so the chromosome names match exactly.

I hope that solves the problem.

All the best,

Steven

aturocks commented 3 years ago

Hi Steven,

Yes - that was the problem. Thank you very much!

Best, Atreyo

StevenWingett commented 3 years ago

Excellent