Hi, I'm looking for an aligner that reports multiple/all hits rather than just a single one. I know mrfast or BWA-short can do this for Illumina data, but is there any aligner that can do this that works on non-Illumina reads? My searches haven't turned up anything.
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What type of non-Illumina reads? There are now a few categories out there. mrFAST should work for Ion Torrent. If you are using pacbio, the blasr parameter -bestn limits the number of hits you will get, up to 2^32 - 1.
Originally posted by Rocketknight View Post -
Good point. I'm interested in 454/Ion Torrent or PacBio reads, so thanks for the info! I didn't realize mrfast could handle Ion Torrent reads, they're pretty specific about calling it an Illumina read aligner on their site. I'll give it a try though!Comment
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Have you tried using other aligners with parameters optimized for returning all hits like bowtie2 (-a), bwa mem (-a), novoalign (-r All) and tmap (mapall)? ThanksComment
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Oh god, I'm sorry. I kept looking through that manual and never saw that. Sorry!Comment
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Glad it helped :-)Comment
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CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
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