I am trying to convert a BAM file to Bigwig using the Convert Format
option under Attributes (I click on the pencil next to the file name
in my history)
The conversion fails with the error message:
11L3_v3 is not found in chromosome sizes file.
11L3_v3 is a genomic sequence ID for the genome that the BAM file
represents. The genome I need is not in the list of Database/build
option in Galaxy. How do I get my conversion to work?
I have uploaded the fasta file for my genome into my history but I do
not see a way to point the conversion tool to that file. Am I on the
Cheers from a Galaxy Newbie!
First, add the genome to the list of Custom Builds for your account.
form to do this is under "User -> Custom Builds". The .fasta version
the genome is one entry option, so go ahead and use that. Pick a name
and a unique "key" that will not conflict with other genomes already
Galaxy (a full list can be viewed by clicking on the link around the
middle of this form, "Show loaded, system-installed builds").
Once the load execution is started, this will take some time to
"process" - how long depends roughly on the size of the genome. After
added, you will be able to assign the build to datasets just like any
other builds that are system-installed. Assign this to your dataset,
then try the tool again.
I am also running a test as a double check that there are no problems
with the method (have not attempted this since our move to the new
hardware a few months ago), but do not anticipate problems. Should an
issue occur, I will write you to follow up.
Meanwhile, you should go ahead and proceed as well. Having your custom
genome set up this way is useful for other reasons (visualization,
general data tracking, etc.).