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Paired end information removed after trimming #1

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mdehollander opened this issue Jul 9, 2012 · 1 comment
Closed

Paired end information removed after trimming #1

mdehollander opened this issue Jul 9, 2012 · 1 comment

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@mdehollander
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Hi, I am using the trimfq function of seqtk on a set for paired end fastq data, but I notice that the paired end information is removed from the header after trimming. Is is possible to keep the header intact during trimming? The header is composed of read information, then a space, and then some more information like the paired end data: Example:
@TJH-ST1807:96:D0YGJAKXX:7:1101:2703:1986 2:N:0:CAAGTA

End after trimming:
@TJH-ST1807:96:D0YGJAKXX:7:1101:2703:1986

Thanks!
cjfields pushed a commit to cjfields/seqtk that referenced this issue Dec 17, 2012
add comment in, addresses github issue lh3#1
7fa574f
cjfields pushed a commit to cjfields/seqtk that referenced this issue May 28, 2013
Revert "add comment in, addresses github issue lh3#1". This clobbers …
0b6c0e8 
…some

changes added at a later point.  Will reapply specific changes in next
commit.

This reverts commit 7fa574f.
cjfields pushed a commit to cjfields/seqtk that referenced this issue May 28, 2013
reapply fix for trimfq, fix for github issue lh3#1
f1254e3
@lh3
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lh3 commented Jul 8, 2013

I have just merged Vince's pull request. Sorry for the delay.

@lh3 lh3 closed this as completed Jul 8, 2013
@aleimba aleimba mentioned this issue Dec 17, 2013
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@mdehollander @lh3