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Old 10-21-2016, 10:29 AM   #15
Location: Fargo

Join Date: Dec 2011
Posts: 66

I am playing with a unix-based option right now. I made a short test list of names in a file test.txt

@HWI-D00653:49:H2FF5BCXX:2:1101:1631:2117 1:N:0:ATCACG
@HWI-D00653:49:H2FF5BCXX:2:1101:1631:2117 2:N:0:ATCACG trim=1
@HWI-D00653:49:H2FF5BCXX:2:1101:1804:2196 1:N:0:ATCACG
@HWI-D00653:49:H2FF5BCXX:2:1101:2187:2119 1:N:0:ATCACG

and am trying to see if I can regenerate a fastq file from it using the command
grep -A 3 test.txt concated.fastq >out.fastq

If it works, I can generate a unique list using grep|sort|uniq

My guess is this could take a while though as the test.txt has been running for the last 5 minutes
horvathdp is offline   Reply With Quote