Retain BED6 format?

[aseveritt]

Hi Noam!

I'm running a lot of bedtools intersect commands that I would love to replace with gia, but I was relying on the information in the bed6 format being retained.

e.g. fileA.bed
chr1 29300 29400

e.g. fileB.bed
chr1 29301 29400 CTAACTTTCCTATCAT-1 41 +
chr1 29328 29427 CTAACTTTCCTATCAT-1 40 -

e.g. output I need with the cell barcode.
chr1 29301 29400 CTAACTTTCCTATCAT-1 41 +

In this case, would I need to use bedrs instead of gia & create an interval type with my additional field?
-- Amanda

[aseveritt]

Ah, sorry just saw issue #50 and #53. I assume that would solve this question too.

[noamteyssier]

Hey Amanda,

This is actually a different issue of mixing file formats (in this case bed3 and bed6). It's on my docket but I haven't had time to work on it yet.

A hacky workaround that you can use to use it immediately is to just make a pseudo bed6 from your bed3:

awk 'OFS="\t"{print $1, $2, $3, 0, 0, "+"}' < fileA.bed > fileA.bed6 

and then to process the bed files with the bed6 input format (the -T flag) you can run:

gia intersect -a fileA.bed6 -b fileB.bed -T bed6

Hopefully that should work for your use case.

It adds an extra step which is kind of annoying but my plan is to have both the inter-format comparisons built and auto-determining input format built after Thanksgiving.

[aseveritt]

Thank you!! That workaround totally works for me.

[noamteyssier]

This took way longer than I wanted but this functionality has been added without the workaround in #112