converting allvalidpairs to pairs

[ratheraarif]

Is there a way to convert allvalidpairs file to pairs file. Actually I need to do some analysis for which I need pairs files but I only have allvalidpairs files.

Best Regards

[nservant]

Yes, that's pretty straightforward. Please look at https://github.com/nf-core/hic/blob/master/modules/local/hicpro/hicpro2pairs.nf

[ratheraarif]

Thank you

[ratheraarif]

This requires going through the nextflow pipeline. Can I do it without going through nf

[nservant]

of course, this is why I put a link to the source code. Basically, in the script section of the nf code, you have the bash command to use to generate the pairs file. You can do it manually ...

[ratheraarif]

Thank you

[ratheraarif]

I got the following error when I try to convert validpairs to pairs

[ti_index_core] the chromosome blocks not continuous at line 7, is the file sorted? [pos 59]

[nservant]

I guess you need to sort the pair file per chromosome coordinate first

[ratheraarif]

Actually I am new to this pipeline. I would appreciate if you point to some pointers for this.

[ratheraarif]

I used the following command to sort the allvalidpairs file sort -V -t $'\t' -k 2,2 -k 5,5 -k 3,3 -k 6,6 "filename.allValidPairs" > filename2.allValidPairs

and the hicpro2pairs script worked well.

Am I missing anything here?

[nservant]

Why do you have a $ in your command ?

[ratheraarif]

Just to show that it is a tab delimited file.

Do I need to change it?

However, I see that removing the $ does not affect the result.. please clarify if I am missing anything here.

Also I want to know that, Do I have to sort the validPairsFile before generating hic or cool file? I am a little fuzzy there.

[nservant]

Which version of pairix are you using ? I had in mind that with the most recent version, the file didn't need to be sorted. That's why I think we commented the sort command in the nextflow code. Anyway, I think it's worth trying both approaches (with or without sort with a recent pairix version)

[ratheraarif]

Program: pairix (PAIRs file IndeXer) Version: 0.3.8

The output of pairs looks like this.

I think I am missing the 11th and 12 th column in the pairs file generated out of the hicpro2pairs.