find overlapping transcripts

Question

[robinycfang]

Hi,

I used stringtie and scallop to assemble transcripts from a few RNAseq samples. Both tools generated annotated and novel transcripts in GTF format. I want to see the overlaps in annotated and novel transcripts between stringtie and scallop. Any recommendation for some handy tools? p.s. have looked at gffcompare, but it seems to work only on overlaps between a reference annotation and your sample gtf.

Thanks!

Answer 1

[Istvan Albert]

bedtools and bedops are the tools most often used to compare interval datatypes:

bedtools: a powerful toolset for genome arithmetic

• https://bedtools.readthedocs.io/en/latest/

BEDOPS: the fast, highly scalable and easily-parallelizable genome analysis toolkit

• https://bedops.readthedocs.io/en/latest/

Answer 2

[Alex Reynolds]

$ bedmap --echo --echo-map <(gtf2bed < annotated.gtf) <(gtf2bed < novel.gtf) > answer.bed

• https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html • https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html