I MiSeqed heterogeneous templates amplified via rolling cycle amplification (RCA) by a specific 6-nt primer. PE reads were merged into single ones around 500 nt. As a consequence of RCA, some of them consist of 100-200 nt repeats from short-size templates. Is anyone aware of tools that can process, extract, and consensus these kinds of reads? Many thanks.
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You could take an example sequence and then use "bbduk.sh" from BBMap suite in filter mode to extract reads containing that sequence with "literal=sequence_you_want" option. Guide to use bbduk is here. -
I believe that is what I want. Thanks!Comment
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GenoMax: Can I extract/separate reads with 0, 1, or 2 motifs (the motif is the same)? Could BB scripts do this job?Comment
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Possibly. You will have to play with parameters for bbduk.sh. "0" should be easy to get.Comment
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Okay, I will try. ThanksComment
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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).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM
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