Existing Approaches For Rna-Seq Reads Aligning To Multiple Gene Loci?

Question

[Tianyang Li]

Hi,

What are some existing approaches for RNA-Seq reads aligning to multiple gene loci?

It seems that most of such reads are discarded, are there any approaches?

Thanks!

Answer 1

[JC]

In general, Bowtie, BWA and others aligners discard reads with more than 10 hits, but you can define the maximal number of hits to be discarded. After that, Cufflinks can deal defining the total reads from each region.