SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
TopHat Error: Could not find Bowtie index files /bowtie-0.12.5/indexes/. rebrendi Bioinformatics 11 06-22-2016 09:55 AM
soap2 PE results do not match bowtie or novoalign axiom7 Bioinformatics 0 01-26-2011 12:43 PM
Different results produced by tophat? kentnf Bioinformatics 2 10-29-2010 09:35 AM
TopHat fails to catch error thrown by Bowtie, gives incomplete results anecsulea Bioinformatics 3 06-06-2010 10:54 AM
TopHat: the results confused me Maria_Lu Bioinformatics 2 05-14-2010 06:54 PM

Reply
 
Thread Tools
Old 07-22-2009, 07:30 PM   #1
baohua100
Senior Member
 
Location: Canada

Join Date: Jun 2008
Posts: 103
Default Tophat and Bowtie results

i have reads.fq (5 000 000 reads RNA-seq) genome.fa

when i use bowtie align the reads, it aligns 4 200 000 reads.

but when i use tophat align the reads, the output file accepted_hits.sam only contains 1 900 000 reads. junctions.bed file is blank.
baohua100 is offline   Reply With Quote
Old 08-11-2009, 08:49 PM   #2
chengeng
Member
 
Location: china

Join Date: Jul 2009
Posts: 14
Default

Hi,
Could you tell me the parameters you set?
chengeng is offline   Reply With Quote
Old 08-11-2009, 08:52 PM   #3
baohua100
Senior Member
 
Location: Canada

Join Date: Jun 2008
Posts: 103
Default

default parameter


tophat ref.fasta reads.fq
baohua100 is offline   Reply With Quote
Old 08-19-2009, 10:41 AM   #4
sorrychen
Junior Member
 
Location: LA

Join Date: Aug 2009
Posts: 9
Default

I also have similar question of inconsistent number of mapping, probably because the parameter setting. Any suggestion about setting the parameter in bowtie/tophat so I can take advantage of the long reads while allowing more mismatches. The /tmp/segments_juncs.fa only have 45bp. How can I use longer reads to map to the junction?
sorrychen is offline   Reply With Quote
Old 08-19-2009, 05:04 PM   #5
chengeng
Member
 
Location: china

Join Date: Jul 2009
Posts: 14
Default

Hello,
You can send E-mail to Cole Trapnell(cole@cs.umd.edu). He is the author of TopHat and Bowtie.

All the best,

Geng
chengeng is offline   Reply With Quote
Old 08-19-2009, 05:06 PM   #6
chengeng
Member
 
Location: china

Join Date: Jul 2009
Posts: 14
Default

Hello,
You can email Cole Trapnell(cole@cs.umd.edu).He is the author of TopHat and Bowtie.

All the best,

Geng
chengeng is offline   Reply With Quote
Old 08-26-2009, 11:17 PM   #7
sorrychen
Junior Member
 
Location: LA

Join Date: Aug 2009
Posts: 9
Default

Thanks, and sorry about the late response. I was told (and confirmed by the options) that Tophat cut long reads into smaller pieces to find junction. In this way, 45 bp junctions will be enough. I think the design is try to avoid there are super small exon that is smaller than 45 bp. If so, a 100 bp reads may mapped to 3 exons.
sorrychen 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 08:49 PM.


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