Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation

Similar Threads
Thread Thread Starter Forum Replies Last Post
Can Cuffdiff treat paired-end and single-end reads at the same time? zun RNA Sequencing 3 06-12-2012 05:37 PM
Can paired-end mapping produce more reads than single-end ? warrenemmett Bioinformatics 13 03-20-2012 11:10 PM
paired-end reads mapped to genome.. gene with only one direction of paired-end reads? danwiththeplan Bioinformatics 2 09-22-2011 02:06 AM
RNA-seq: Replicates, single-end, paired-end story pasta Bioinformatics 2 07-04-2011 11:51 PM
Does Cufflinks support single-end and paired end data together ? ersenkavak Bioinformatics 1 10-22-2010 07:26 AM

Thread Tools
Old 05-14-2010, 06:26 AM   #1
Junior Member
Location: Germany

Join Date: May 2010
Posts: 1
Default actual paired-end distances

I have got an Illumina run of paired-end 500 and 100 bases length. A couple of programs want to know minimum and maximum distance. What are reasonable values here?
There is also often the relative orientation of the readpairs, like forward forward or forward backward. Would this be forward backward for a paired-end protocol?
steuerna is offline   Reply With Quote
Old 05-17-2010, 10:43 AM   #2
Senior Member
Location: Boston area

Join Date: Nov 2007
Posts: 747

The actual distances will depend on your library prep.

At least some aligners will infer the distance from data; even if not, you can always align in single-end mode (perhaps on a sample of the data), compute the required statistics & then run the full-blown alignment
krobison 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 04:07 PM.

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