How can I check for library composition bias RNA-seq data

Question

[debitboro]

Hi Biostars,

I'm looking for a method by which I can check the library composition bias in my RNA-seq data ?

thanks in advance

Answer 1

[BioinfGuru]

Run FASTQC + MULTIQC initially to look for things like GC bias and overrepresented sequences. You should know when your library was fragmented from the RNA-seq method. That will give a clue as to which end may be lower quality. QC will help with identifying this and knowing what to trim. After mapping you can also measure library complexity but that is further down the road.