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Old 06-12-2019, 06:56 PM   #1
fanx
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Default Extract reads contains repeats

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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Old 06-13-2019, 02:42 AM   #2
GenoMax
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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.
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Old 06-13-2019, 09:21 AM   #3
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I believe that is what I want. Thanks!
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Old 06-15-2019, 01:03 PM   #4
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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?
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Old 06-15-2019, 04:32 PM   #5
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Possibly. You will have to play with parameters for bbduk.sh. "0" should be easy to get.
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Old 06-15-2019, 05:18 PM   #6
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Okay, I will try. Thanks
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