Question: View bam files on UCSC genome browser (Galaxy display application)
gravatar for yliu41
16 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 • 682 views
ADD COMMENTlink modified 16 months ago by Jennifer Hillman Jackson25k • written 16 months ago by yliu4150
gravatar for Jennifer Hillman Jackson
16 months ago by
United States
Jennifer Hillman Jackson25k 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 16 months ago by Jennifer Hillman Jackson25k

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 16 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 16 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 169 users visited in the last hour