Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: local galaxy tophat2 built-in genome
0
gravatar for biowz
3.4 years ago by
biowz • 0
United States
biowz • 0 wrote:

Hi,

I am new user to do bioinformatic analysis and know a little about python. Right now, I succeed adding bowtie2- human genome index, and bowtie2 can recognize this built-in genome, however tophat2 can not recognize it.I do not know how to make a path to fix this. Would you like showing me steps in detail? Thank you very much!

 
tophat software error galaxy • 847 views
ADD COMMENT • link •
modified 3.4 years ago by Bjoern Gruening ♦ 5.1k • written 3.4 years ago by biowz • 0
0
gravatar for Bjoern Gruening
3.4 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi!

You can install the bowtie2 data manager from the TS: https://toolshed.g2.bx.psu.edu/view/devteam/data_manager_bowtie2_index_builder this should update all indexes automatically.

Ciao,

Bjoern
ADD COMMENT • link written 3.4 years ago by Bjoern Gruening ♦ 5.1k

Hi,

Thank you very much for your help. I installed data_manager_bowtie2_index_builder before. I used this tool to add bowtie2 human reference index. Bowtie2 software can recognize this index well, however tophat2 can not did this. I also re-install data_manager_bowtie2_index_builder again. It is still no any change. Would you like to help me thinking about it again. Thank you very much in advance!

 

 

 

ADD REPLY • link written 3.4 years ago by biowz • 0
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: 179 users visited in the last hour