SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Average Read Coverage for 454 paired end read data lisa1102 Core Facilities 8 10-18-2011 08:40 AM
Paired end Short read data SS1234 Bioinformatics 6 06-09-2010 01:16 PM
help! what is a paired-end read? hitdavid Bioinformatics 1 01-14-2010 11:42 AM
Difference in paired-end and single-end read ? darshan Bioinformatics 1 09-30-2009 11:44 PM

Reply
 
Thread Tools
Old 10-26-2015, 10:40 AM   #81
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,553
Default

Quote:
Originally Posted by mido1951 View Post
yes I know.
I'm talking of phase before getting contigs.
you know to make an assembly of reads that it must overlap.
In the case of paired end reads, how to find overlaps between the two files?
we F1.fq that contains reads RX.1 and F2.fq that contains reads RX.2.
how to find the overlap between these reads? is what we should do a merging between RX.1 and RX.2?
So the merging is necessary?
thanks
It's very simple. You do this:

bbmerge.sh in1=F1.fq in2=F2.fq out=merged.fq outu=unmerged.fq
Brian Bushnell is offline   Reply With Quote
Old 10-26-2015, 10:46 AM   #82
mido1951
Senior Member
 
Location: Tunisia

Join Date: May 2014
Posts: 116
Default

thanks for your answer.
So, the merging is necessary ??
thanks
mido1951 is offline   Reply With Quote
Old 10-26-2015, 10:46 AM   #83
Brian Bushnell
Super Moderator
 
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,553
Default

No, merging is optional.
Brian Bushnell is offline   Reply With Quote
Old 10-26-2015, 10:51 AM   #84
mido1951
Senior Member
 
Location: Tunisia

Join Date: May 2014
Posts: 116
Default

if the merging is optional,
how to do overlap reads without merging the two files into one file??
mido1951 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 11:29 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO