Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

How to take "HiC-Pro validPairs file" as input #18

Open
rysterzhu opened this issue Sep 27, 2019 · 1 comment
Open

How to take "HiC-Pro validPairs file" as input #18

rysterzhu opened this issue Sep 27, 2019 · 1 comment

Comments

@rysterzhu
Copy link

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
Copy link
Member

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.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants