SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
bowtie error: extra parameters specified BioSlayer Bioinformatics 1 10-07-2011 10:38 AM
Wrong of Tophat's bowtie parameters, a bug chenyao Bioinformatics 3 08-23-2011 05:06 AM
Bowtie parameters khb Bioinformatics 11 12-16-2010 09:08 PM
BWA, BOWTIE: what parameters for different analysis (ChIP, RNA, miRNA etc) dukevn Bioinformatics 2 08-12-2010 09:57 AM
Recommended Bowtie Parameters agc SOLiD 0 05-10-2010 03:44 AM

Reply
 
Thread Tools
Old 02-18-2010, 02:56 PM   #1
deepsea
Member
 
Location: California

Join Date: Jan 2010
Posts: 12
Default Tophat's bowtie parameters

Hi folks,

I am using tophat in my RNA-seq of a high polymorphic genome. I think Tophat calls bowtie with '-v 2', but I found many reads with more than 2 mismatches were mapped to the genome. I took one as the test, it has 5 mismatches with good phred quality scores:

13:C>T,27:C>A,38:T>C,57:G>A,64:C>A

Using -v 3, or default -n 2 -l 28 -e 70 cannot map it, but using -n 2 -l 28 -e 150 can map it.

Why can tophat map these kind of reads?

Thanks!
deepsea is offline   Reply With Quote
Old 02-28-2010, 06:18 PM   #2
Gangcai
Member
 
Location: Shanghai, China

Join Date: Nov 2009
Posts: 30
Default

I also have a quite similar question: How to set the other bowtie parameters in tophat(such as "-a --best --strata")?
Gangcai is offline   Reply With Quote
Old 02-28-2010, 08:57 PM   #3
Xi Wang
Senior Member
 
Location: MDC, Berlin, Germany

Join Date: Oct 2009
Posts: 317
Default

Quote:
Originally Posted by Gangcai View Post
I also have a quite similar question: How to set the other bowtie parameters in tophat(such as "-a --best --strata")?
I did it just by editing the python script of tophat.
__________________
Xi Wang
Xi Wang is offline   Reply With Quote
Old 03-03-2010, 11:05 AM   #4
thinkRNA
Member
 
Location: Carlsbad,CA

Join Date: Jan 2010
Posts: 94
Default

Quote:
Originally Posted by Xi Wang View Post
I did it just by editing the python script of tophat.
How exactly did you do this? Which line and what is the name of the script?

I appreciate your help in advance. Thanks !
thinkRNA is offline   Reply With Quote
Old 03-03-2010, 04:21 PM   #5
Gangcai
Member
 
Location: Shanghai, China

Join Date: Nov 2009
Posts: 30
Default you can modify the tophat bin file

The file you should modify is tophat-1.0.13/bin/tophat. I have an example file in the attached file for my question(add --best, --strata and --seedmms)(the modified line have #by gangcai)

After modification, you can run tophat like this:

$tophat --best --strata --seedmms 3 ......

Quote:
Originally Posted by thinkRNA View Post
How exactly did you do this? Which line and what is the name of the script?

I appreciate your help in advance. Thanks !
Attached Files
File Type: tar tophat.tar (70.0 KB, 184 views)
Gangcai is offline   Reply With Quote
Old 03-03-2010, 04:30 PM   #6
Xi Wang
Senior Member
 
Location: MDC, Berlin, Germany

Join Date: Oct 2009
Posts: 317
Default

Quote:
Originally Posted by Gangcai View Post
The file you should modify is tophat-1.0.13/bin/tophat. I have an example file in the attached file for my question(add --best, --strata and --seedmms)(the modified line have #by gangcai)

After modification, you can run tophat like this:

$tophat --best --strata --seedmms 3 ......
Great! I think tophat developers should also take those options into consideration.
__________________
Xi Wang
Xi Wang is offline   Reply With Quote
Old 09-20-2010, 02:42 PM   #7
peromhc
Senior Member
 
Location: Durham, NH

Join Date: Sep 2009
Posts: 108
Default

I agree, one of the strengths of BOWTIE is being able to modify the way it works via its options- but all of this customizability is lost when using TOPHAT..
peromhc is offline   Reply With Quote
Old 02-25-2011, 08:29 AM   #8
joseph
Member
 
Location: ca

Join Date: Feb 2008
Posts: 39
Default help with Tophat's bowtie parameters

Quote:
Originally Posted by Gangcai View Post
The file you should modify is tophat-1.0.13/bin/tophat. I have an example file in the attached file for my question(add --best, --strata and --seedmms)(the modified line have #by gangcai)

After modification, you can run tophat like this:

$tophat --best --strata --seedmms 3 ......

Hi
If it is not too much trouble, can you post a tophat file with modification to the the latest version (1.2). My data maps better when I set my own -n/--seedmms and -l/--seedlen parameters.
As you can tell, I don't know how to write scripts.

Thank you in advance

Joseph Dhahbi
joseph is offline   Reply With Quote
Old 02-25-2011, 08:02 PM   #9
Xi Wang
Senior Member
 
Location: MDC, Berlin, Germany

Join Date: Oct 2009
Posts: 317
Default

Quote:
Originally Posted by joseph View Post
Hi
If it is not too much trouble, can you post a tophat file with modification to the the latest version (1.2). My data maps better when I set my own -n/--seedmms and -l/--seedlen parameters.
As you can tell, I don't know how to write scripts.

Thank you in advance

Joseph Dhahbi
I think the authors of Tophat don't want users to run Tophat in this way. One of the reasons should be that those parameters also apply to segment mapping in Tophat. A segment is an arbitrary part of a read, not necessarily from the left end of a read. So the seed region of a segment could be different from the seed of a whole read. This may cause some biases, I guess.
__________________
Xi Wang
Xi Wang is offline   Reply With Quote
Old 07-05-2011, 06:19 AM   #10
shrutiisarda
Junior Member
 
Location: Atlanta

Join Date: Jun 2011
Posts: 2
Default TopHat source code modification to include --best

Hi all,

I want to use TopHat for my mRNA Seq analysis, but I am unable to include --best..

I tried modifying the code to include best (similar to what's given above), but I was not successful..

Could someone please provide a modification in the latest version (1.3.1)? *I wish tophat did not make it impossible to edit bowtie options on the command line*
shrutiisarda is offline   Reply With Quote
Old 07-08-2011, 04:39 AM   #11
blue mood
Member
 
Location: China

Join Date: Jul 2011
Posts: 22
Default

i have another problem about tophat.
i mapped 90bp pair-end reads twice with tophat of different versions with same arguments -g 10 -r 20 --solexa1.3-quals .The default segment-mismatch is 2. in the otput of the older version(1.0.12),the minimum match length is 75bp,why?. in the output of the latest version(1.3.1) it is mostly 90bp, is it because the -v 2 ?
is there anyone facing the same problem?
blue mood is offline   Reply With Quote
Old 07-14-2011, 05:14 PM   #12
DineshCyanam
Compendia Bio
 
Location: Ann Arbor

Join Date: Oct 2010
Posts: 35
Default

Shrutii,
U can try a different approach... Might work... If u have already run tophat... there is a log folder in the output directory. Open run.log file. It lists the sequence of commands tophat executes... I think there are 29 steps totally. U can modify the steps in which bowtie is called and give the --best flag... and then run all the commands as a bash script but as Xi Wang mentioned above, I too feel Cole or the other authors of Tophat do not want users to run it this way. I might be wrong tho...

Dinesh

Quote:
Originally Posted by shrutiisarda View Post
Hi all,

I want to use TopHat for my mRNA Seq analysis, but I am unable to include --best..

I tried modifying the code to include best (similar to what's given above), but I was not successful..

Could someone please provide a modification in the latest version (1.3.1)? *I wish tophat did not make it impossible to edit bowtie options on the command line*
DineshCyanam 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 02:23 PM.


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