Hi Kelly,

Checking to see if you have an update on the following issue from last week. I had shared this history with you last week.

SAM-to-BAM conversion tool has two options “locally cached” or “history” and neither of those allows me to change/select a specific genome build.

Thanks,

Hemant

From: Kelly Vincent [mailto:kpvincent@bx.psu.edu]
Sent: Friday, April 15, 2011 2:35 PM
To: Kelkar, Hemant
Cc: galaxy-user@bx.psu.edu
Subject: Re: [galaxy-user] SAM to BAM conversion problem

Hemant,

This is really odd, and definitely not what should be happening. Would you mind sharing your history with me so I can take a closer look? 

While I'm looking into it, you should be able to manually change the database to ce6 and then run SAM-to-BAM. We have everything needed for ce6.

Thanks,

Kelly

On Apr 15, 2011, at 12:55 PM, Kelkar, Hemant wrote:

Hello Galaxy Support,

I generated an alignment with a “fastq groomed” illumina dataset using the “Map with BWA” tool in galaxy with the “C. elegans ce6” genome. Interestingly the results (when I click on the history name) say that the database used was “ce7”. When I try to use the “SAM-to-BAM” tool, I am getting a “sequences are not currently available for specified build” error.

Thanks,

Hemant

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