Hello biostar,
I am currently working on differential expression analysis of mRNA data, I have two questions and I need your help and your expertise.
I did a mapping on the reference genome by STAR and I need to quantify also the multi-mappers reads.
my first question:do you think featureCounts is reliable for quantifying multimapper reads with the -M option?
my second question: what do you think if I do the quantification at -g exon-id instead of -g gene-id, (because it interests me only the exons ). I used both parameters and I noticed a decrease of 2% in number of reads quantify when I used -g exon-id.
Thank you, Kamel
I already used --quantMode with star, it gives directly the quantification level gene_id and I'm not sure if it quantify ambiguity or not, for other sofwtare you mentioned I can't use it because I want a mapping on the genome not on the transcriptome.
Could you answer me on my question if I can use featureCount -M option and my 2nd question if you have an answer. Thank you
I updated my answer.
No, STAR with
--quantMode GeneCounts
does not count multi-mapping reads.You are mapping to the genome, but summarizing over genes, so mapping / counting over the transcriptome and summarizing over genes with tximport would result in exactly the same genes being summarized.
Thank you for your answer I will try to use them. what do you think about the software mmquant ??
It just so happens we had the very same question earlier today, here is the answer:
C: using two read counting methods with RNA-seq