Mapping genomic sequence reads to transcriptome reference?

[hbn]

Hello,

I would like to know whether it would be sensible to map genomic sequence reads to a reference transcriptome for SNP and indel calling. I would think that this is not a very good idea, but I don't have any experience to back this up. Of course, due to your intron-exon boundaries you would get a lot of read clipping. I am hoping someone has experience with this saying whether this yields any good results.

The obvious solution seems to be to assemble the genomic sequence reads, but due to the size and complexity of the genome this does not yield anything valuable.


Any input is appreciated, thanks!

[brianytsui]

It depends in large on the question that you are trying to address. For example, just like what u suggested, intron-exon could be a concern if u are worried abt the SNPs at the splice junctions, where mapping to reference transciptome simplify this issue as it supposedly provides all the full transcripts, but has the problem of high read to target position multi-mapping if the tool is not adjusted for that.

But you are not familiar with how the tools behave, I would highly recommend to go with GATK RNA-seq SNP calling pipeline.