View bam files on UCSC genome browser (Galaxy display application)

Question: View bam files on UCSC genome browser (Galaxy display application)

16 months ago by

yliu41 • 50

yliu41 • 50 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:="" wiki.galaxyproject.org="" Learn="" Datatypes#BAM"="" rel="nofollow">https://wiki.galaxyproject.org/Learn/Datatypes#BAM">
  <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"/>
</datatype>

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

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modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 16 months ago by yliu41 • 50

16 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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: http://hgdownload.soe.ucsc.edu/downloads.html

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

Hope this helps! Jen, Galaxy team

ADD COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 16 months ago by yliu41 • 50

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 REPLY • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k

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