Using Agrep With 2 Patterns

Question

[toshnam]

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

Answer 1

[Giovanni M Dall'Olio]

Just use .* instead of ;.

The following should work:

agrep -1 'AGGATT.*GGCGAT' sample.fa

[toshnam]

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?

[Giovanni M Dall'Olio]

http://www.regular-expressions.info/reference.html