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Old 02-13-2019, 11:14 PM   #30
tolot27
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Location: Germany

Join Date: Jan 2012
Posts: 3
Default deinterleave with singletons

Hi!

I have a interleaved fastq containing unmapped reads produced by segemehl -u. I want to deinterleave it into the two mate pair files as well as removing/saving the singletons into a separate file.

Currently, reformat.sh cannot deal with it, even if I give outsingle= as parameter. The header contains the strand information (i. e. 2:N:0:2).

Is there some way to get at least the pairing reads extracted without singletons in between?

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Kind regards,
Mathias
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