SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Assembly (velvet) of mate-pair data from Illumina Protaeus Bioinformatics 2 03-26-2012 05:13 AM
Rescuing Orphaned reads with local alignment within a radius of mapped mate apratap Bioinformatics 0 06-29-2011 09:46 AM
How to check if reads are properly paired in mate-pair data? genepool_bee Bioinformatics 2 02-22-2011 01:07 AM
mate pair + single read data boetsie General 1 04-14-2010 09:08 AM
Closing gaps using Solexa mate-pair data maasha Bioinformatics 3 08-27-2009 07:52 AM

Reply
 
Thread Tools
Old 12-14-2011, 10:59 AM   #1
weeseda
Junior Member
 
Location: Alabama, US

Join Date: Dec 2011
Posts: 5
Default Rescuing mate-pair data

Hello all,

We recently had trouble with the sequencing facility we use and got a bad batch of genomic runs back that I would like to attempt to “rescue” and assemble. The runs should have been mate-paired reads of 100 bases with a 3kb insert on an Illumina sequencer (one whole lane/sample). However, there was a problem when the data was taken off the machine and one set of reads is incomplete. The one set (e.g. right) of reads came off alright (100 bases of high quality each), but the other reads (e.g. left) were cut short ~45 bases (each read has 55 high quality bases followed by 45 Ns). So we basically have reads of 100 bases mate-paired with reads of only 55 bases and a 3kb insert.

Any suggestions on possible ways to rescue these genomic runs?

Thanks in advance for any suggestion,
David
weeseda is offline   Reply With Quote
Old 12-14-2011, 11:36 AM   #2
swbarnes2
Senior Member
 
Location: San Diego

Join Date: May 2008
Posts: 912
Default

55 bases should be enough to align correctly, so I think it should still work out alright.
swbarnes2 is offline   Reply With Quote
Reply

Tags
assemble, genomics, illumina, mate-paired reads, research solution

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 12:33 PM.


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