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,
Jane
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,
Jane
Comment