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Using Agrep With 2 Patterns

Hi,

I want to extract reads containing both 5'- and 3'- flanking sequences accepting 1 mismatches from raw fastq files. I guess it filter 'AGGATTACGTGGCGAT' out in raw fastq, but below command doesn't work.

$ agrep -1 'AGGATT;GGCGAT' sample.fa

How can I fix the command?

Thanks.
S. Nam

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updated by Giovanni M Dall'Olio Giovanni M Dall'Olio • written by toshnam toshnam

1 answer

Just use .* instead of ;.

The following should work: 

agrep -1 'AGGATT.*GGCGAT' sample.fa
• 135 views • link
written by Giovanni M Dall'Olio Giovanni M Dall'Olio

Thank you for your comment. I found ';' means 'and' operator in google. Where can I get an information like operator '.*'? How did you know about that?

• 0 views • link
written by toshnam toshnam

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