Question: Tophat2 index problem
1
gravatar for yasser.morsy
2.3 years ago by
yasser.morsy10
yasser.morsy10 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 • 1.4k views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by yasser.morsy10

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 REPLYlink written 2.3 years ago by Jennifer Hillman Jackson25k

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

ADD REPLYlink written 2.3 years ago by yasser.morsy10
0
gravatar for yasser.morsy
2.3 years ago by
yasser.morsy10
yasser.morsy10 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 COMMENTlink written 2.3 years ago by yasser.morsy10
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