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Old 04-03-2013, 08:39 AM   #5
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,087

Originally Posted by Amative View Post
I tried to blast the first ten reads from one of the samples I have, blast results were not that good.
You probably want to go into the file some ways. With illumina atleast the first hundred (or more) sequences may not represent the best of the lot since they are generally from the edge of the flowcell/start of the lane.

You may also want to use this tool to do some screening: http://www.bioinformatics.babraham.a.../fastq_screen/
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