How to get transcripts counts from STAR

Question

[Triple Nipple]

Hello,

After successful runs of STAR, in the ReadsPerGene.out.tab file, I only have counts of Genes (ENSG/ENSMUSG) and I don't have counts of transcripts (ENST/ENSMUST), which I need.

My STAR index genome was obtained by reference genome from ENSEMBL and the .gtf annotation files were achieved from ENSEMBL.

This should be simple, but I can't figure it out. How can I achieve this?

Thanks

Answer 1

[h.mon]

You can't get transcript counts directly from STAR. You have to output the BAM aligned to the transcriptome (option --quantMode TranscriptomeSAM) and then use RSEM, eXpress or Salmon to perform the quantification.