Problem with bedtools intersect with two gtfs
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Entering edit mode
19 months ago
newbie ▴ 100

I'm trying to use bedtools intersect on gencode annotation gtf and another gtf which is output from stringtie merge option.

bedtools intersect -v -b gencode.v27.annotation.gtf -a stringtiemerge.gtf > final.gtf

This is how gencode gtf looks:

enter image description here

And this is how the stringtie merged gtf looks:

enter image description here

But when I used bedtools intersect, I see there is warning. I can understand that it is because of the contigs which are not found in gencode gtf. So, the below warning, should I consider that or no need to care?

bedtools intersect -v -b gencode.v27.annotation.gtf -a stringtiemerge.gtf > final.gtf

***** WARNING: File stringtiemerge.gtf has inconsistent naming convention for record:
GL000008.2  StringTie   transcript  1577    8168    .   +   .   transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; xloc "XLOC_000001"; class_code "u"; tss_id "TSS1";

***** WARNING: File stringtiemerge.gtf has inconsistent naming convention for record:
GL000008.2  StringTie   transcript  1577    8168    .   +   .   transcript_id "MSTRG.4.1"; gene_id "MSTRG.4"; xloc "XLOC_000001"; class_code "u"; tss_id "TSS1";
RNA-Seq gtf bedtools intersect • 665 views
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Entering edit mode

perhaps because the order of the attributes is unexpected? in the file you have gene_id followed by transcript_id, the warning shows it flipped. It shouldn't matter but it might.

(BTW including the a few lines from the data instead of images would make more sense)

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