De-Multiplexing MiSeq Data

[abh]

Hi,

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
CTCGGT
+
<@@DFD

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?

[GenoMax]

Check post #7 in this thread: http://seqanswers.com/forums/showthread.php?t=22407 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.

[sklages]

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 :-)