Question: View bam files on UCSC genome browser (Galaxy display application)
gravatar for yliu41
4 months ago by
yliu4150 wrote:

Hello folks,

I want to view BAM files on UCSC genome browser. I got my BAM files from HISAT2. But I don't see a link for viewing them on UCSC genome browser. I saw there is bam.xml in /display_applications/ucsc/. And in datatypes_conf.xml.sample, it shows bam can display on ucsc:

<datatype extension="bam" type="galaxy.datatypes.binary:Bam" mimetype="application/octet-stream" display_in_upload="true" description="A binary file compressed in the BGZF format with a '.bam' file extension." description_url="&lt;a href=" https:="""" Learn="" Datatypes#BAM"="" rel="nofollow">">
  <converter file="bam_to_bai.xml" target_datatype="bai"/>
  <converter file="bam_to_bigwig_converter.xml" target_datatype="bigwig"/>
  <display file="ucsc/bam.xml"/>
  <display file="ensembl/ensembl_bam.xml"/>
  <display file="igv/bam.xml"/>
  <display file="igb/bam.xml"/>
  <display file="iobio/bam.xml"/>

Why there is no ucsc link for viewing bam? Did I miss any configuration? Thank you in advance!

bam • 198 views
ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson23k • written 4 months ago by yliu4150
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson23k wrote:


Assign a database to the dataset that matches a UCSC genome "dbkey". For example, human data could be assigned "hg19" or "hg38".

First, check if your database/genome is hosted at UCSC. Review genomes and discover the dbkey choices here:

Second, assign the database/genome by clicking on the pencil icon on the dataset's top upper right corner and assign. How to: > How do I find, adjust, and/or correct metadata?

Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 4 months ago by Jennifer Hillman Jackson23k

Thank you Jen! It is very helpful!

I have another question: my database is mm10, but it is not in Galaxy dataset's metadata (database/build). I found mm9 in it. How can I add mm10 to Galaxy? Thanks a lot.

ADD REPLYlink written 4 months ago by yliu4150

You will need to add the mm10 genome with Data Managers (the one I linked that includes dbkey creation is the correct DM to start with). - Jen

ADD REPLYlink written 4 months ago by Jennifer Hillman Jackson23k
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