SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Fusion gene detect tools for Solid (colorspace)single end 50bp RNA-seq data yinxiaohe RNA Sequencing 3 08-22-2011 07:04 PM
small test data set for genomic SOLiD paired-end sequencing? sdvie Bioinformatics 4 02-15-2011 12:19 AM
Single-end SOLiD data for TopHat wlnjseu RNA Sequencing 6 10-15-2010 02:28 AM
GC coverage bias: difference between 2008 (36mers) and 2010 (75mers) data BaCh Illumina/Solexa 13 05-19-2010 12:53 PM
Difference in paired-end and single-end read ? darshan Bioinformatics 1 10-01-2009 12:44 AM

Reply
 
Thread Tools
Old 04-22-2011, 02:18 AM   #1
ryuky
Junior Member
 
Location: china

Join Date: Mar 2011
Posts: 7
Default What's the difference between the Solid F5-P2 and R3 end data?

What's the difference between the Solid F5-P2 and R3 end data?
In order to use the BWA solid2fastq.pl I must have the R3 ended data, so how can I just transform the F5-P2 to R3?
ryuky is offline   Reply With Quote
Old 04-22-2011, 04:57 AM   #2
kopi-o
Senior Member
 
Location: Stockholm, Sweden

Join Date: Feb 2008
Posts: 319
Default

You should be able to just change all occurrences of "F5-P2" to "R3".
kopi-o is offline   Reply With Quote
Old 04-22-2011, 08:45 AM   #3
ryuky
Junior Member
 
Location: china

Join Date: Mar 2011
Posts: 7
Default

Quote:
Originally Posted by kopi-o View Post
You should be able to just change all occurrences of "F5-P2" to "R3".
I think the F5-P2" and "R3" are totally different! One comes from the same +strand with the F3 file(R3) and the other come from the reverse strand.
you could see the ABI's protocol for construct the mate-pair library
ryuky is offline   Reply With Quote
Old 04-22-2011, 09:07 AM   #4
kopi-o
Senior Member
 
Location: Stockholm, Sweden

Join Date: Feb 2008
Posts: 319
Default

Sure, R3 is for a mate-pair run and F5-P2 is for a paired-end run, but for making the fastq files this doesn't matter. Right?
kopi-o is offline   Reply With Quote
Old 04-22-2011, 09:06 PM   #5
ryuky
Junior Member
 
Location: china

Join Date: Mar 2011
Posts: 7
Default

Quote:
Originally Posted by kopi-o View Post
Sure, R3 is for a mate-pair run and F5-P2 is for a paired-end run, but for making the fastq files this doesn't matter. Right?
yeah, I have read this script,
first I think the script will translate the mate-end R3 to the complementary trand because F3 and R3 come from the same strand and next step we must use the paired-end, which come from different strand, to do BWA aln. But I think this script don't do this.
ryuky 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 06:05 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO