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Old 02-07-2018, 03:54 AM   #1
k_a_r_o_l
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Default Removing reads with repeats

Hello,

Can anyone help me. In my data I have reads like:

CACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACACCCAC

ACACACACACACACACAC

CACACACACACACAC


They are in different versions and lenght.

How can I eliminate them? Any sostware, command?
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Old 02-07-2018, 03:58 AM   #2
GenoMax
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What is the data format, fastq or fasta?
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Old 02-07-2018, 03:59 AM   #3
k_a_r_o_l
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fastq files
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Old 02-07-2018, 04:11 AM   #4
GenoMax
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You can use bbduk.sh from BBMap suite. Use "literal=CACACACACACA k=7" in addition to input output options.

Let me know if you need more help.
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Old 02-07-2018, 10:08 PM   #5
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Thx. for help

Finally I used SGA preprocess with --dust option and I think it helped.
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