I am trying to analyse RNA-seq data and I want to use a gtf annotation file of RepeatMasker to quantify the reads, but I am finding one problem with all annotation files from UCSC RepeatMasker: every single file contain repeated sequences identifiers (transcript_id por example). I do not know how to deal with it, because I found on another post that this file does not have problems: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/rmsk.txt.gz. However, I have tried to convert it into a valid format for featureCounts function through many ways but I have not been capable of it. I would appreciate whatever new idea or alternative.
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frarodmar17 •
2 answers
You can convert the RM output (https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.out.gz) to a valid GTF with some script but I guess featureCounts will have problems assigning reads as they will map to multiple locations.
I recommend the Hammell lab GTF files:
Basically reformatted rmsk into a more logical GTF. Gene id is the element name and individual loci are transcript ids. It also keeps track of "family" and "class".
Otherwise, I recommend reformatting the rmsk into SAF format.
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