How to take "HiC-Pro validPairs file" as input

[rysterzhu]

The column 5 in .tsv input file, you said it means "length1: how many bases were mapped (integer)".
I don't understand it much.

I use HiC-Pro pipeline which output a *allValidPairs file , it has the following columns
"read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]"
Is it possible covert this file to .tsv file?

[yannickspill]

length1 is the number of bases that were mapped from read 1 to the genome. Usually, it is reported by the mapper, now I don't think it is reported in this output. What you can do, is set it to the read size, as found in the fastq file.