Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Merge variable-length adaptor from beginning of read sowalsky Bioinformatics 0 11-12-2012 12:27 PM
Demultiplexing in-line barcodes saikumarkv Illumina/Solexa 6 03-28-2012 02:07 PM
tophat, --mate-inner-dist and variable length reads dawe Bioinformatics 2 01-20-2012 04:47 AM
Variable length paired-end read processing using Cufflinks ZhengXia Bioinformatics 0 10-03-2011 08:23 AM
Software for variable-length PE reads shazzle Bioinformatics 1 11-15-2010 09:51 PM

Thread Tools
Old 08-10-2013, 12:36 PM   #1
Senior Member
Location: USA

Join Date: Sep 2012
Posts: 130
Default Demultiplexing using variable-length barcodes

Is there a tool for demultiplexing using variable-length barcodes? If it makes any difference, the barcodes are within the read, not a separate read.

My personal solution would be to demultiplex in multiple steps, starting with the longest barcodes. Is there a better option? There are a lot of demultiplexing tools. Surely one of them supports barcodes of different lengths.
id0 is offline   Reply With Quote
Old 08-10-2013, 02:46 PM   #2
Senior Member
Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381

you can use jMHC.
You will have to make separate de-multiplexing passes though.
The program is a lot faster on Mac than PC/Ubuntu for some reason but is easy to use and produces good output excel files.

Also, depending on your data set size, you may need to open jMHC/java from the terminal - allocating more RAM. I can get though ~ 2M reads in a couple of hours
JackieBadger is offline   Reply With Quote

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 07:21 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO