Question: Bam To Bigwig
0
gravatar for Susanne Warrenfeltz
4.6 years ago by
United States
Susanne Warrenfeltz40 wrote:
Hello, 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 right track? Cheers from a Galaxy Newbie! Susanne
galaxy • 4.6k views
ADD COMMENTlink modified 4.6 years ago by Jennifer Hillman Jackson25k • written 4.6 years ago by Susanne Warrenfeltz40
0
gravatar for Jennifer Hillman Jackson
4.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Susanne, First, add the genome to the list of Custom Builds for your account. The form to do this is under "User -> Custom Builds". The .fasta version of 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 in 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.). Best, Jen Galaxy team -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD COMMENTlink written 4.6 years ago by Jennifer Hillman Jackson25k
Clicked submit Thanks! To: Susanne Warrenfeltz; galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] bam to bigwig Hello Susanne, First, add the genome to the list of Custom Builds for your account. The form to do this is under "User -> Custom Builds". The .fasta version of 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 in 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.). Best, Jen Galaxy team Hello, 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 right track? Cheers from a Galaxy Newbie! Susanne ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org
ADD REPLYlink written 4.6 years ago by Susanne Warrenfeltz40

Dear Jennifer,

I have a question regarding the IGV and bigwig conversion that maybe you can help me. I am trying to convert a .bam file to bigwig with mouse genome (mm10) to visualize the reads and I am getting this error:

hashMustFindVal: 'GL456210.1' not found

and this is my command:

wigToBigWig  -clip mm10.chrom.sizes ./control1.bw

I already found out that I need to convert the chromosome Ids to UCSC. I want to know is this common to convert the IDs from ENSEMBLE to UCSC for bigwig conversion? Do you have any idea about it?

Many Thanks in advance,

RSH

ADD REPLYlink written 3.2 years ago by rahel143500
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