Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Tophat2 index problem
1
gravatar for yasser.morsy
2.6 years ago by
yasser.morsy • 10
yasser.morsy • 10 wrote:

I'm trying to align RNA-seq data of wheat genome so i used bowtie2 with large index option to build the genome index and the results was formated as bt2l instead of bt2 but when i'm running tophat it gives me that error

[2016-04-29 01:29:37] Beginning TopHat run (v2.1.0)

[2016-04-29 01:29:37] Checking for Bowtie Bowtie version: 2.2.6.0 [2016-04-29 01:29:37] Checking for Bowtie index files (genome).. Error: Could not find Bowtie 2 index files (reference_in.*.bt2)

If i changed the format dose it will work accurately and if not please suggest a solution for that problem.
rna-seq tophat • 1.7k views
ADD COMMENT • link •
modified 2.6 years ago • written 2.6 years ago by yasser.morsy • 10

Hello - This seems like a problem - it was brought up once before but not resolved. We'll do some more testing and reply with feedback (likely a bug ticket).

Thanks for reporting the issue. Jen, Galaxy team

ADD REPLY • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

thank you Jennifer i figured out by changing the script to read bt2l instead of bt2 and that solved the problem

ADD REPLY • link written 2.6 years ago by yasser.morsy • 10
0
gravatar for yasser.morsy
2.6 years ago by
yasser.morsy • 10
yasser.morsy • 10 wrote:

Thank all I had tried to change the tophat script in the usr/bin from reading bt2 to bt2l and it worked well
ADD COMMENT • link written 2.6 years ago by yasser.morsy • 10
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 168 users visited in the last hour