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06-12-2019, 07:56 PM
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#1 |
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Member
Location: USA Join Date: Sep 2012
Posts: 22
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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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06-13-2019, 03:42 AM
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#2 |
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Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,091
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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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06-13-2019, 10:21 AM
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#3 |
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Member
Location: USA Join Date: Sep 2012
Posts: 22
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I believe that is what I want. Thanks!
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06-15-2019, 02:03 PM
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#4 |
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Member
Location: USA Join Date: Sep 2012
Posts: 22
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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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06-15-2019, 05:32 PM
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#5 |
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Senior Member
Location: East Coast USA Join Date: Feb 2008
Posts: 7,091
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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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06-15-2019, 06:18 PM
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#6 |
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Member
Location: USA Join Date: Sep 2012
Posts: 22
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Okay, I will try. Thanks
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