I'm trying to put genes from ENCODE and NONCODE in one gtf file and filter out NONCODE genes which are already in Encode. My bedtools command is:
bedtools intersect -wa -a NONCODE.gtf -b Gencode_exon.gtf -v -s -f 0.9
(I only take "exon" features from Gencode, otherwise it removes more transcripts from NONCODE)
This works okay for the most part but if I have overlapping transcripts in my NONCODE file, I get only one exon in the output:
Does anybody have any idea why does it happen and how to fix it? I can use another tool, just need to make sure I get all the Gencode genes and only the transcripts from NONCODE which don't completely (90%) overlap with Gencode. It has to be strand-specific too.