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Old 05-10-2016, 01:52 AM   #1
Jane M
Senior Member
Location: Paris

Join Date: Aug 2011
Posts: 239
Question Which feature file for htseq-count for non coding elements of ribodepleted samples?

Dear all,

Sorry if this question has been asked before, I have not found similar topics on the web, but there are probably...
Until now, I used a gtf downloaded from UCSC table (genome: human, assembly: hg19, group:genes and gene predictions, track: RefSeq genes, table: refFlat) as a feature file, with gene name, in GFF format for counting reads in genes with htseq-count.
I have one experiment with ribodepleted samples (TruSeq total RNA Stranded). I first counted the reads and performed differential expression analysis using such a gtf. In this gtf downloaded few weeks ago, there are 26688 genes, including 913 "LINC*". This number of lincRNA seems low, so I wonder if this table is comprehensive for ribodepleted experiment.
Can you please tell me which reference you use when interesting in non coding elements of ribodepleted experiments?

Thank you for your feedback,
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