Hi All,
I am going to check mapped reads that I got from tophat, and I want to use IGV to look for specific genes names in my data . In my case ,I have to create .genome file in IGV because I used the reference genome and the annotation file from Ensemble .
I tried to creat my .genome file on IGV, I found that in IGV user guide I should have the annotation file as .BED format. so is there any simple tool to convert gtf to bed format.
2 answers
You can use BEDOPS gtf2bed, e.g., $ gtf2bed < my_data.gtf > my_data.bed
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written
by
Alex Reynolds
You can use a GTF file in IGV for the annotation. In fact, that's the most common method.
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written
by
Devon Ryan
That's unusual. I've done this exact thing before and not had issues. Perhaps something is wonky with the GTF.
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written
by
Devon Ryan
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Hello M K!
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