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Old 11-20-2018, 10:27 AM   #1
RamP
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Location: Hyderabad

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Default Aligner for PacBio RNASeq

I am wondering if I can use BLASR for aligning RNASeq reads from Human cell lines. I am interested in identifying the splice sites. I read this paper "Evaluation of tools for long read RNA-seq splice-aware alignment" (Bioinformatics, 2018) where different splice aware tools were compared and concluded GMAP to be the best among the compared ones. However, they didn't include BLASR in their evaluation. Could the reason be that BLASR is suitable only for genomic read alignments? Thanks.
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