SEQanswers

Go Back   SEQanswers > Applications Forums > De novo discovery



Similar Threads
Thread Thread Starter Forum Replies Last Post
paired-end read length for de novo assembly Seqasaurus Illumina/Solexa 4 10-19-2011 03:32 AM
Illumina de novo assembly with quality values Peter Bjarke Olsen Bioinformatics 2 06-21-2010 02:11 AM
Read length for Illumina mate pairs Linnea Illumina/Solexa 2 06-08-2010 11:46 PM
De novo fragment assembly with short mate-paired reads, Does the read length matter? strob Literature Watch 3 10-23-2009 01:36 PM
De novo short read assembly? Which assembler is the best? Patrick De novo discovery 0 06-23-2009 06:42 PM

Reply
 
Thread Tools
Old 11-16-2009, 11:40 AM   #1
bkingham
Member
 
Location: delaware

Join Date: May 2008
Posts: 11
Default de novo assembly and Illumina read length

We are preparing to do paired-end de novo sequencing on our GAIIx with the new kits. Is there a reason to run less than the maximum 100+ cycles on each end? There was a suggestion that the higher error rates at 100+ may make <100 cycles more desirable. My thoughts are more is better, particularly b/c a majority of the cost is linked to cluster generation.
bkingham is offline   Reply With Quote
Old 11-16-2009, 11:15 PM   #2
francesco.vezzi
Member
 
Location: Udine (Italy)

Join Date: Jan 2009
Posts: 50
Default

Quote:
Originally Posted by bkingham View Post
My thoughts are more is better
This is usually true but if the more you produce is meaningless it is only a waste. For example one year ago we produce with the kit of 36 bases experiments of 45 bases with the result that we where oblige to throw away all the bases after the 36 ....

If the kit is able to produce 100 bases that you have to produce only 100 and be happy if all the 100 bases are of good quality and can be used

Francesco
francesco.vezzi 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 08:08 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO