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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Is there any description about the .allValidPairs? #338

Closed LeopoldC closed 4 years ago

LeopoldC commented 4 years ago

Hi Nicolas, I want to convert the result of read mapping output, is there any description of each column of the .allValidPairs file somewhere? Didn't find it in the manual.

Best Léopold

nservant commented 4 years ago

Hi Léopold, https://nservant.github.io/HiC-Pro/RESULTS.html#list-of-valid-interaction-products But it is not upd-to-date :)

read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size / res_frag1/ mapq1 / res_frag2 / mapq2 [/ allele_specific_tag]

N

LeopoldC commented 4 years ago

perfect thanks, sorry to didn't find it :D

hanshanmengqi commented 11 months ago

Hi @nservant, I just wonder the pos_reads1 means the start of read1 position? Another point, the fragment_size means the length of read1 and read2?

Thank you for your time. Best, Han