quantifying transcripts in a redundant genome

[garlic]

Hi,

I am trying to quantify the number of reads mapping to genes in a highly redundant bacterial genome (i.e., often several exact gene copies in the genome).

I've mapped reads to genes with bbmap, and quantified using featurecounts. My problem is that reads are only counted for one of the copies of redundant genes, and not all of them.

I just want to count the number of expressed genes (I want to count all of the copies since I can't distinguish them). I've tried playing around with multi-mapping parameters in featurecounts, but nothing has changed.

Does anyone here know how to do this?

Thanks!

[ASintsova]

You would have to play with your aligner (bbmap). I've never used that one before, but other aligners like bowtie2 and BWA have an option to search for multiple alignments and report all. However, if you do this, you will be overestimating expression of your redundant genes.