Question: Tophat Problem On A New Local Instance
0
gravatar for Elwood Linney
5.0 years ago by
Elwood Linney180
Elwood Linney180 wrote:
I have installed a local instance of Galaxy as a one user in a Mac Pro desktop. I got some valuable help from Dannon Baker regarding how to load large datasets into it. However I noticed that the Upload file for this instance would only go up to the Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) version of the zebrafish assembly while where as the online version went up to the newer assembly zebrafish assembly Jul. 2010 (Zv9/danRER7) While I could download newer reference genome in the program from UCSC Main table browser whenever the local instance offered alternatives for genomes it only went up the earlier version (Zv8/danRer6) (danRer6) . I went ahead anyway, groomed 4 x 16gb datasets but when it came to Tophat, An error occurred with this dataset: Could not determine Tophat version /bin/sh: tophat: command not found Error indexing reference sequence /bin/sh: bowtie-build: command not found Also, when I download from UCSC the most updated zebrafish genome reference sequence and use it for Tophat, I get the following error signal: I don't know if this issue of assembly version is associated with my Tophat problem--the two Tophat screens I get from either the main Galaxy or my instance are attached for comparison: my local instance does not give me a "Use built-in genome option" while the main Galaxy does Any advice? Elwood Linney DUMC
alignment bowtie • 804 views
ADD COMMENTlink written 5.0 years ago by Elwood Linney180
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 118 users visited in the last hour