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!
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!
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