SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
how --mate-inner-dist and --mate-std-dev affect the tophat mapping result liuxq Bioinformatics 0 11-06-2011 08:53 PM
Variable length paired-end read processing using Cufflinks ZhengXia Bioinformatics 0 10-03-2011 08:23 AM
Software for variable-length PE reads shazzle Bioinformatics 1 11-15-2010 09:51 PM
How does inner distances(--mate-inner-dist and --mate-std-dev) work in tophat? Gangcai Bioinformatics 4 06-15-2010 05:53 AM
Tophat and cufflinks mate-inner-dist option combiochem Bioinformatics 2 04-22-2010 05:02 PM

Reply
 
Thread Tools
Old 01-20-2012, 03:44 AM   #1
dawe
Senior Member
 
Location: 4530'25.22"N / 915'53.00"E

Join Date: Apr 2009
Posts: 258
Default tophat, --mate-inner-dist and variable length reads

Hi there, I have variable length RNA-seq reads ranging from 42 to 76 bp (I guess because of a trimming process). Since I have to specify --mate-inner-dist parameter, which would be the correct value?
Any hint is appreciated

d
dawe is offline   Reply With Quote
Old 01-20-2012, 04:43 AM   #2
kmcarr
Senior Member
 
Location: USA, Midwest

Join Date: May 2008
Posts: 1,165
Default

Quote:
Originally Posted by dawe View Post
Hi there, I have variable length RNA-seq reads ranging from 42 to 76 bp (I guess because of a trimming process). Since I have to specify --mate-inner-dist parameter, which would be the correct value?
Any hint is appreciated

d
I would suggest using some average value (mean, median, whatever) for --mate-inner-distance and accompanying that with an appropriate --mate-std-dev.
kmcarr is offline   Reply With Quote
Old 01-20-2012, 04:47 AM   #3
dawe
Senior Member
 
Location: 4530'25.22"N / 915'53.00"E

Join Date: Apr 2009
Posts: 258
Default

Good point, thanks!
Besides... I've realized I must know what trimming process has been applied. If 5' trimming, the inner size remains the same, if 3' trimming I will try to evaluate mean/stddev

d
dawe is offline   Reply With Quote
Reply

Tags
rna-seq, tophat

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 10:24 PM.


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