A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hello Everyone,
I have been trying to use the .pairs files (output in *`results/hicpro/valid_pairs/pairix`*) for downstream analysis, but it seems that the pair files that i am generating don't have the proper header for the 4DN format. I believe that the header is not being generated at all in the  `<http://hicpro2pairs.nf|hicpro2pairs.nf>` module, but i am not too sure. Any help will be appreciated.

```##columns: readID chr1 pos1 chr2 pos2 strand1 strand2
    awk '{OFS="\t";print \$1,\$2,\$3,\$5,\$6,\$4,\$7}' $vpairs | bgzip -c &gt; ${prefix}_contacts.pairs.gz
    ##sort -k2,2 -k4,4 -k3,3n -k5,5n ${prefix}_contacts.pairs | bgzip -c &gt; ${prefix}_contacts.pairs.gz
    pairix -f ${prefix}_contacts.pairs.gz```


Hi, which tools did you use for downstream analysis ? could you open an issue on the nf-core-hic about that please ;)