convert UTR.bed file to .gft

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3.6 years ago

Goback • 0

Hi Biostars,

I downloaded the 5'UTR and 3'UTR bed file from the UCSC genome browser, then I used "bedToGenePred" and "genePredToGtf" to convert the bed file to gft file for featurecounts. after I got the gft file, I found the UTR regions were re-annotated as exon, CDS, transcripts, which made me confused. if I want to count reads mapping to the UTR region, shall I count all these features and then sum the result?

Thank you.

RNA-Seq • 838 views

ADD COMMENT • link 3.6 years ago by Goback • 0

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Why can't you use featureCounts with a GTF file with all annotations and count 3'-UTRs (three_prime_utr) and 5'-UTRs (five_prime_utr)?

ADD REPLY • link 3.6 years ago by jkkbuddika ▴ 190

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The annotation file (gencode.v33.annotation_comprehensive.gtf) doesn't provide features like 3'UTR and 5' UTR.

ADD REPLY • link 3.6 years ago by Goback • 0

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Is there a problem with using annotations from Ensembl? The nice thing for you is that the GTF file already contains all the annotations you need.

If you want to get your approach to work there are other methods to convert bed files to GTF and are described in this post.