Hello,
I used tophat on mapping of RNA-seq samples, after running TopHat I got accepted_hit.bam file. Is it possible to use this BAM on the variant call analysis using Samtools? I overheard that BAM from TopHat is not good to variant call, but I don't know the reason. Which are alignment tools good for RNA-seq to do the variant call?
many thanks,
I used tophat on mapping of RNA-seq samples, after running TopHat I got accepted_hit.bam file. Is it possible to use this BAM on the variant call analysis using Samtools? I overheard that BAM from TopHat is not good to variant call, but I don't know the reason. Which are alignment tools good for RNA-seq to do the variant call?
many thanks,
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