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
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 http://usegalaxy.org, 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
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