Hey friends,
I have two accepted_hits.bam
files one for RNA-seq and another for ribo-seq produced by tophat2. Today my adviser asked me how I can count the number of reads that have mapped to the each gene. I searched in biostars posts but I could not figure out yet. Can you help me please?
Thank you
http://lmgtfy.com/?q=site%3Abiostars.org+number+reads+gene
Thank you Pierre for your complete guidance!
You are going to have plenty of tools to do that (like this answer). The real question is, what and how are you counting exactly? You can count only uniquely mapped reads, reads that fall entirely into exons of your genes or just overlap them etc... You may also want a way to normalize your values (say, using FPKM).
This gets messy: ask your PI what exact method you should use. Ideally, you might find an article on the subject you are researching whose Materials and Methods RNASeq section can be recycled - you will be able to make more rigorous comparisons of your finds and those of the articles.
At minimum, you will need an annotation file with the position of the features you are counting.
thank you cyril-cros