SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat: options -N --read-edit-dist --read-gap-length Pradhaun Bioinformatics 0 01-04-2013 08:58 AM
tophat seq length qual length mismatch error epi Bioinformatics 3 09-10-2012 02:43 AM
picard error: Mismatch between read length and quals length writing read shawpa Bioinformatics 0 08-20-2012 06:52 AM
Tophat 1.3.0 max-deletion-length option BUGFIX andrewmagis Bioinformatics 3 06-18-2011 12:07 AM
TopHat: output is not recognized by UCSC geriatrics1200 RNA Sequencing 2 11-06-2009 11:13 AM

Reply
 
Thread Tools
Old 07-10-2013, 01:54 PM   #1
eric.yu
Junior Member
 
Location: Midwest

Join Date: Jul 2013
Posts: 2
Default tophat: option --read-gap-length not recognized?

Hi,

I'm really new to this so please bear with me if I made some really silly mistakes.

Here's my code for tophat:
tophat -p 8 --bowtie1 -G path --no-novel-juncs --read-mismatches 4 --read-gap-length 3 --read-edit-dist 2 -o path path &

and it gave me error :
tophat: option --read-gap-length not recognized

Any advice'd be appreciated thanks!

Last edited by eric.yu; 07-10-2013 at 02:11 PM.
eric.yu is offline   Reply With Quote
Old 07-10-2013, 03:45 PM   #2
chadn737
Senior Member
 
Location: US

Join Date: Jan 2009
Posts: 392
Default

1) What version of tophat are you running.....are you sure you have tophat2? Try typing tophat --version to see what version you have.

2) Secondly, that command wouldn't work anyhow. --read-mismatches and --read-gap-length cannot exceed the value of --read-edit-dist. If you want to set the read-mismatches to 4 an --read-gap-length to 3, then you also have to set the read-edit-dist to 4 or more.

Last edited by chadn737; 07-10-2013 at 04:16 PM.
chadn737 is offline   Reply With Quote
Old 07-11-2013, 07:10 AM   #3
eric.yu
Junior Member
 
Location: Midwest

Join Date: Jul 2013
Posts: 2
Default

Quote:
Originally Posted by chadn737 View Post
1) What version of tophat are you running.....are you sure you have tophat2? Try typing tophat --version to see what version you have.

2) Secondly, that command wouldn't work anyhow. --read-mismatches and --read-gap-length cannot exceed the value of --read-edit-dist. If you want to set the read-mismatches to 4 an --read-gap-length to 3, then you also have to set the read-edit-dist to 4 or more.

Thanks for your reply.
It's 2.0.4
and also tried
tophat -p 8 --bowtie1 -G $home/Genes/genes.gtf --no-novel-juncs --read-mismatches 4 --read-gap-length 3 --read-edit-dist 4 -o $home/C1_thout3 $home/BowtieIndex/genome $home/Sample_C1.R1_trimmed.fq.gz &

still doesn't run
eric.yu is offline   Reply With Quote
Old 07-30-2013, 06:32 PM   #4
jp.
Senior Member
 
Location: NikoNarita.jp

Join Date: Jul 2013
Posts: 142
Question

Hi Senior Member
I have used tophat successfully with default functions. however, this time I got problem. How to give commands for read length 101 x 2 with insert sixe 80~380(main 150) ?
I am totally confused


Quote:
Originally Posted by chadn737 View Post
1) What version of tophat are you running.....are you sure you have tophat2? Try typing tophat --version to see what version you have.

2) Secondly, that command wouldn't work anyhow. --read-mismatches and --read-gap-length cannot exceed the value of --read-edit-dist. If you want to set the read-mismatches to 4 an --read-gap-length to 3, then you also have to set the read-edit-dist to 4 or more.
jp. is offline   Reply With Quote
Old 08-01-2013, 08:38 AM   #5
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

Quote:
Originally Posted by jp. View Post
Hi Senior Member
I have used tophat successfully with default functions. however, this time I got problem. How to give commands for read length 101 x 2 with insert sixe 80~380(main 150) ?
I am totally confused
I presume that you've looked at --mate-inner-distance plus --mate-std-dev and are just having a hard time figuring out that the numbers should be. Here are two relevant seqanswer posts that should help:

http://seqanswers.com/forums/showthread.php?t=4815

and

http://seqanswers.com/forums/showthread.php?t=4355
westerman is offline   Reply With Quote
Old 08-01-2013, 07:19 PM   #6
jp.
Senior Member
 
Location: NikoNarita.jp

Join Date: Jul 2013
Posts: 142
Smile

Thank you so much for your help. I got the answer. negative value can be given for --mate-inner-distance.
Great help for me, thanks


Quote:
Originally Posted by westerman View Post
I presume that you've looked at --mate-inner-distance plus --mate-std-dev and are just having a hard time figuring out that the numbers should be. Here are two relevant seqanswer posts that should help:

http://seqanswers.com/forums/showthread.php?t=4815

and

http://seqanswers.com/forums/showthread.php?t=4355
jp. 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 05:44 PM.


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