Hi, I was wondering if anyone know how to merge 2 or more gff files to make a consensus gff file? I have gtf file from tophat/cufflinks pipeline gff file from velvet assembly and i would like to merge these two to the already annotated gff file. The idea is to have one gff file instead of three gff files so that i can load this as track on my Genome Browser. Thanks in advance
$ for i in `ls *.gtf`; \ do gtf2bed < $i > $i.converted.bed; \ done;
Then do a multiset union set operation with BEDOPS
bedops (link) to make a single BED file called
answer.bed that can be loaded into your genome browser instance:
$ bedops --everything *.converted.bed | cut -f1-6 - > answer.bed
I know you probably figured this out since it was asked 6 years ago but I ended up using gffcompare in 2019 (for anyone else looking for this): https://ccb.jhu.edu/software/stringtie/gffcompare.shtml
It worked really well.
conda create --name gffcompare_env -c bioconda gffcompare -y
(I usually create a separate environment for all my tools to keep things clean. )
The above tool takes in a file with paths to gtf files and then you just specify an output, Se the link for more information on the usage.