SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Should I trim my MiSeq data? cwzkevin Bioinformatics 3 09-06-2012 09:51 AM
Help with De-Multiplexing MiSeq Data Cirno Bioinformatics 8 08-16-2012 01:51 PM
MiSeq Bacterial Genome Multiplexing eosin Illumina/Solexa 4 03-28-2012 05:02 PM
Multiplexing attila.szanto RNA Sequencing 2 12-02-2011 07:32 AM
Multiplexing bioinfosm Illumina/Solexa 0 09-24-2008 09:05 AM

Reply
 
Thread Tools
Old 11-08-2012, 10:23 AM   #1
abh
Member
 
Location: philadelphia

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

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?
abh is offline   Reply With Quote
Old 11-08-2012, 10:58 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,780
Default

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.

Last edited by GenoMax; 11-08-2012 at 11:00 AM.
GenoMax is offline   Reply With Quote
Old 11-09-2012, 04:26 AM   #3
sklages
Senior Member
 
Location: Berlin, DE

Join Date: May 2008
Posts: 620
Default

Quote:
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 :-)
sklages is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:19 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO