Question: visulizion of peak from bamcomparei n UCSC
gravatar for khani.sajjad
3.3 years ago by
khani.sajjad0 wrote:

I am using bamcompare in Galaxy for the first time to normalize the bam file of my chip.seq data. The end bigwig file I got from bamcovrage and bamcompare I can not visualize them in the UCSC genome browse. There is a link for UCSC genome browser and I select mm9 but later in the genome browser it shows no data. sajjd

bamcompare • 987 views
ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by khani.sajjad0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


I am assuming that the custom track displays at UCSC and that you have selected a visualization option other than "Hide". If this is not true, then the pop-up message from UCSC would be good to share. You can also ask the UCSC support team about specific errors (after input format/content is verified).

Did you map against mm9 originally? If not and this database was assigned after the mapping run, then that could be a source of the problem (a chromosome/coordinate mismatch problem). The resolution is to map against the same exact genome that is in use by the target browser (Trackster - internal to Galaxy, UCSC, Ensembl, IGB, etc.).

The other item to check for is the content of the datasets that you are trying to visualize. Do they contain data after normalization? Check the result comments and the file sizes. Or is the data sparse? Perhaps localized to particular genome regions but the UCSC browser was not set to display those regions? 

If you continue to have problems after verifying the genome and the presence of content, then the issue could be server related. If this work was not done at, please try testing there with one of your datasets. If the problem is only at another site or a local/cloudman Galaxy, the problem is likely with configuration on that other server (if another public server, contacting the administrators would be advised).

If the issue is also present on Galaxy Main after these checks, we may ask for you to share a history with the original data to determine the root cause.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k
gravatar for khani.sajjad
3.3 years ago by
khani.sajjad0 wrote:

Hi Jen

Thanks so much for the comprehensive infromation. Now I got the problem. BAM files produced by our bioinformatics facility created by mm10 and I can only select mm9 in the Galaxy/deeptools attributes. But unfortunately I can not change my bam files, and I would like to use mm10 in the bamcoverage/bamcompare attributes, please help me know if there is any option?

thanks and have a nice weekend


ADD COMMENTlink written 3.3 years ago by khani.sajjad0

Hi Sajjad

Are you refereing top "Effective genome size" when you are talking about 'mm10 atributes'? You can select: "user specified" and provide your own number




ADD REPLYlink written 3.3 years ago by Hotz, Hans-Rudolf1.8k

Hi Hans-Rudolf,

Actually I am refering to mouse reference genome. After running bamcompare, I have to set the attribute and in the link named "Database/Build: " I would like to have mm10 as a referece genome but in the option there is only mm7, mm8, and mm9. I really have no idea how to select mm10



ADD REPLYlink written 3.3 years ago by khani.sajjad0

Now, I understand, you are not talking about the atribute of a tool, but about the atribute of the result (ie the history item), aren't-you?

Are you the admin of the galaxy server you are using? If yes, you need t modify tool-data/shared/ucsc/builds.txt by adding: "mm10    Mouse Dec. 2011 (GRCm38/mm10) (mm10)" and restarting the server. If you are not the admin, you need to forward this to her/him.


Hope this helps, Hans-Rudolf

ADD REPLYlink written 3.3 years ago by Hotz, Hans-Rudolf1.8k
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