Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
TopHat Checking for Bowtie [Failed] ercfrtz Bioinformatics 1 03-14-2011 02:43 PM
mapping 454 reads to a reference genome query Bioinformatics 33 02-09-2011 07:36 AM
Bowtie and reads that failed to align: (100.00%) michy Bioinformatics 7 02-08-2011 07:42 PM
TopHat+BWT = reads that failed to align ~ 99% repinementer Bioinformatics 6 09-28-2010 08:31 PM
Difficulty mapping reads with non-reference allele? krobison Genomic Resequencing 3 10-09-2009 11:48 AM

Thread Tools
Old 06-02-2010, 01:33 AM   #1
Location: India

Join Date: Jun 2010
Posts: 20
Default Tophat...Mapping reads against Reference with Bowtie [FAILED]


I am trying to run tophat with the sample data reads_1.fq and reads_2.fq.

I built the bowtie index successfully and moved the generated index files to the Bowtie indexes subdirectory. I run the command

tophat -r 20 test_ref reads_1.fq reads_2.fq

and the output i got is an error showing on console

[Wed Jun 2 13:46:29 2010] Beginning TopHat run (v1.0.7)
[Wed Jun 2 13:46:29 2010] Preparing output location ./tophat_out/
[Wed Jun 2 13:46:29 2010] Checking for Bowtie index files
[Wed Jun 2 13:46:29 2010] Checking for reference FASTA file
[Wed Jun 2 13:46:29 2010] Checking for Bowtie
Bowtie version:
[Wed Jun 2 13:46:29 2010] Checking reads
seed length: 75bp
format: fastq
quality scale: phred
Splitting reads into 3 segments
[Wed Jun 2 13:46:29 2010] Mapping reads against test_ref with Bowtie
Error: could not execute Bowtie
Traceback (most recent call last):
File "/usr/bin/tophat", line 1476, in ?
File "/usr/bin/tophat", line 1450, in main
File "/usr/bin/tophat", line 1297, in spliced_alignment
File "/usr/bin/tophat", line 612, in bowtie
TypeError: 'str' object is not callable

Could you please help me to sort out this issue.

Brajbio is offline   Reply With Quote

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 04:21 AM.

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