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Old 03-02-2015, 03:58 PM   #1
Location: USA

Join Date: Aug 2014
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I have a 3 columns file (conting name, lenght, number of reads).

How can I select the only contigs that are at least 500nt in lenght and that have at least 1000 reads mapping?

Is there a command to do that, even in different steps?

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Old 03-02-2015, 05:10 PM   #2
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If your file is tab separated following will work. If you have some other field separator then change \t accordingly. Following assumes that you only have numbers in columns 2 and 3.

$ awk -F'\t' '{ if ($2 >= 500 && $3 >= 1000) print $0}' your_file
If above does not work then post a small sample of your file.
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Old 03-03-2015, 05:10 AM   #3
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It works perfect!
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