Hello, I have downloaded human transcriptome (RefSeq transcripts) from this website. I want to download gene annotation file for this transcriptome. Can some one help me explaining how to do that?
I tried using ucsc table browser how ever seems like I am downloading a wrong file. Because, when I use that gtf file to count raw counts from aligned RNA-seq data (aligned to human transcriptome) I get zero for all of the transcripts.
Which genome build did you use for your alignment?
you can download the annotation file from ensembl FTP
I have attached the link above from where I downloaded the human transcriptome. build 38
What exactly you downloaded,
Reference Genome Sequenceor
RefSeq Transcripts? How did you map and count?
I used STAR aligner for mapping with human transcriptome from the link above without gene annotation file. I tried to get the total count using RseQC.