How can I map sRNAs (20-30nt) to a reference, knowing that there are gaps in the sRNA?
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BBMap should be able to handle that without much trouble; it allows gaps in very short reads. How long do you expect the gaps to be? -
I guess also hundreds of nt compared to the reference, but it's just a speculation.. thanksComment
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If you expect them to be hundreds of nt (which seems unlikely to me... normally small RNA introns, if present, are very short) you can try this:
bbmap.sh ref=ref.fa in=reads.fq out=mapped.sam maxindel=500 tipsearch=500 k=11 slow
The slow flag, longer-than-default tipsearch, and most importantly shorter-than-default k will greatly slow it down (particularly on a large genome), but should ensure that you capture all the introns in those very short reads. Be sure to adapter-trim them prior to mapping.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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