Hi all
I would like your input on software to use for SNP calling from a pooled transcriptome sample, I have a whole genome (Eucalyptus grandis).
The problem is the incorporation of splice junctions into my pipeline.
-What should I map with? (so far I'm thinking Tophat)
-What can I use for calling of SNPs? (As Tophat produces a BAM file this should be easy)
All advice welcome. PS I'm working with Illumina paired end reads
I would like your input on software to use for SNP calling from a pooled transcriptome sample, I have a whole genome (Eucalyptus grandis).
The problem is the incorporation of splice junctions into my pipeline.
-What should I map with? (so far I'm thinking Tophat)
-What can I use for calling of SNPs? (As Tophat produces a BAM file this should be easy)
All advice welcome. PS I'm working with Illumina paired end reads
Comment