Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
SFF Read names johan 454 Pyrosequencing 8 04-19-2012 08:54 AM
Bowtie changes read names in SAM output ashish Bioinformatics 9 07-22-2011 01:33 PM
Simulated reads mapping to same region - maq simulate & dwgsim gprakhar Bioinformatics 2 02-19-2011 12:12 AM
Mosaik - Read Names Trimmed sichan Bioinformatics 0 01-26-2011 01:20 PM
Run maq on solexa data with simulated qual scores AnamikaDarwin Bioinformatics 0 05-22-2009 11:52 AM

Thread Tools
Old 11-18-2010, 07:46 PM   #1
Location: CSHL

Join Date: Nov 2009
Posts: 15
Default MAQ simulated read header names


I'm using MAQ to simulate reads and I was hoping someone could shed some light on how the read names are generated. It looks as though the name is something like:
(coordinate name)_(start position in the coordinate)_(stop position in the coordinate)_(hexadecimal number for the read)/(1/2)
Since the reads are simulated as mate pairs, (stop position - start position + 1) is the outer distance of the insert sizes, which will vary based on the desired mean outer distance of insert sizes and its standard deviation. I looked around MAQ's documentation to see if they described the method, but I had no luck. Does anyone happen to know if this is the naming convention?

MBekritsky is offline   Reply With Quote

maq, simulate, simulating sequence data

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 11:05 PM.

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