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Old 11-08-2012, 11:23 AM   #1
Location: philadelphia

Join Date: Aug 2012
Posts: 13
Default De-Multiplexing MiSeq Data


I have 3 fastq files consisting of R1, R2 read files and
a separate index file. for example They are in the format below.

R1: @M00132:6:000000000-A0JG4:1:1:18014:1842 1:N:0:0
Sequence data

R2: @M00132:6:000000000-A0JG4:1:1:18014:1842 2:N:0:0
Sequence data

Index: @M00132:6:000000000-A0JG4:1:1:18014:1842 1:N:0:0

I want to split the R1 and R2 files based on this barcode.
and create new files that contain these barcodes

does any script or tool avaliable online so that i can work on it?
abh is offline   Reply With Quote
Old 11-08-2012, 11:58 AM   #2
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,080

Check post #7 in this thread: There is a script there that you may need to tweak for your files.

FYI: As you create a new thread SeqAnswers does an automatic search on your post and then suggests past threads that may help. Look for them in the "Similar Threads" section at the top.

I am still baffled as to why sequencing facilities hand out sequence data without completing the de-multiplexing.

Last edited by GenoMax; 11-08-2012 at 12:00 PM.
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Old 11-09-2012, 05:26 AM   #3
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Location: Berlin, DE

Join Date: May 2008
Posts: 628

Originally Posted by GenoMax View Post
I am still baffled as to why sequencing facilities hand out sequence data without completing the de-multiplexing.
Maybe he should just ask. Sometimes customers don't mention anything about indices ... bad luck if these samples are put on a SE run. But as PE runs are much more frequent nowadays (at least in our environment), it shouldn't be much of a problem.

my 2p :-)
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