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RNAseq variant calling from HISAT and Trinity aligners
I want to perform variant calling on my RNAseq dataset and I got stuck at the Split'N'Trim pre-processing step, as I want to apply the same (or similar) pipeline to two sets of reads:
1. aligned to a reference genome (with HISAT2)
2. aligned to a reference transcriptome (using Trinity/Bowtie2)
In your RNAseq Best Practices you suggest the usage of mapping quality reassignment, however, HISAT2 already reassigns this score from 255 to 60. In this context, is it really necessary to specify this parameter?
How about Trinity alignments, do you have any suggestions on how to procceed?