Genome with many duplicated genes: allow multimapping in featurecounts?

Question

[Tatiana]

Hi everyone,

I am wondering if I should allow multi-mapping in featurecounts if I work with a fish genome and it has high gene duplication level. I need to align illumina RNA-seq reads to genome and obtain counts.

The featurecounts tutorial doesn't say anything about it. It says only: "We recommend that reads or fragments overlapping more than one gene are not counted for RNA-seq experiments, because any single fragment must originate from only one of the target genes but the identity of the true target gene cannot be confidently determined. On the other hand, we recommend that multi-overlapping reads or fragments are counted for ChIP-seq experiments because for example epigenetic modifications inferred from these reads may regulate the biological functions of all their overlapping genes."

Any suggestions?

Answer 1

[swbarnes2]

Mapping won't so much be your problem as assigning reads to genes.

Use RSEM to assign reads to genes instead. Rather than ignoring multi-mappers, it tries to work out the odds of where the reads are likely to really come from.