How to add a genome indexed at https://usegalaxy.org to IGB (when it is not already natively included)

Question: How to add a genome indexed at https://usegalaxy.org to IGB (when it is not already natively included)

7 months ago by

kelly.871 • 0 wrote:

Hello,

I have been using Galaxy Main to map WGS data from E. coli. I have tried several mapping approaches against the eschColi_K12 reference and I think the sequencing data is mapping correctly (From bam.iobio.io: >99% mapped reads, >95% proper pairs, >40 mapping quality score). However, when I try to view the data in either IGV or IGB, these programs are not locating the eschColi_K12 genome and no sequencing data is showing up. Is there a step I am missing to be able to view my data against the reference? I have made sure the data is sorted and indexed and it hasn't changed the results.

Any help or suggestions will be greatly appreciated.

Thank you

datacache igb genome usegalaxy.org igv • 578 views

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modified 7 months ago by Jennifer Hillman Jackson ♦ 25k • written 7 months ago by kelly.871 • 0

7 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The exact eschColi_K12reference genome indexed at Galaxy Main https://usegalaxy.org can be retrieved from our public data repository. This is how: https://galaxyproject.org/admin/reference-data-repo/

Once you have the fasta dataset, this prior Q&A has details for using it with IGB: https://biostar.usegalaxy.org/p/27494

For others reading, to visualize data that is already included in IGV, open the IGV application first (locally), make sure the database is assigned to your dataset, and an IGV link will become available within the dataset. More details are in this prior Q&A: https://biostar.usegalaxy.org/p/10075/

Thanks! Jen, Galaxy team

ADD COMMENT • link modified 7 months ago • written 7 months ago by Jennifer Hillman Jackson ♦ 25k

Jennifer,

Thank you, I was able to locate and load the eschColi_K12 reference genome so that I am no longer getting the notice that my genome ID doesn't match. I still am unable to view my data on either IGV and IGB (no sequencing data appears). The goal of this alignment was to manually identify variants but since this alignment approach hasn't worked, I also made a vcf file using mpileup SAMtools. The process ran successfully but when I try to view it on IGV, still nothing appears. Do you have any other advice or suggestions on how I can view my data. I have looked at the other post you linked to in your initial response and unfortunately that hasn't helped fixed my problems yet.

Thank you for taking the time to look at my post.

Best, Paul

ADD REPLY • link written 7 months ago by kelly.871 • 0

This sounds odd ... would you please do one of these (your data remains private with either):

Post back here the name of the history and the dataset number of the VCF file that you cannot visualize? This doesn't need to be a history share link, just the names so I can locate the specific data you are having the problem with from the admin side.

Send an email to galaxy-bugs@lists.galaxyproject.org from your registered account email address with the same information. Please include a link to this Biostars post as well so we can link the two.

Thanks and sorry you are still having problems!

ADD REPLY • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k

Jennifer,

I emailed the address you provided and I haven't heard anything back over the last week which is obviously fine because I know everyone is busy. I did want to reach back out to you to see if maybe you could help with my problem.

My history name is "unnamed history" and dataset # 21 contains my VCF file.

Thank you for your continued assistance.

Paul

ADD REPLY • link written 6 months ago by kelly.871 • 0

Hi Paul, this review is on my list. We've had many issues reported while testing the 18.05 pre-release. I'll try to get to this by the end of this week if not sooner. There is probably some genome mismatch issue present, but I'll check to see if that is true or not. Jen

ADD REPLY • link written 6 months ago by Jennifer Hillman Jackson ♦ 25k

Thank you so much for your help!

ADD REPLY • link written 6 months ago by kelly.871 • 0

Well, I had this test running in the background for several hours today. There is definitely a problem, I am just not sure what the source is yet (Galaxy or IGV). Please see this ticket for details: https://github.com/galaxyproject/usegalaxy-playbook/issues/122

VCF data cannot be viewed in IGB and I haven't tested a BAM dataset (expect that to work, no reported problems with BAMs, but a few for VCF files across display applications (iobio; ucsc for certain VCFs).

ADD REPLY • link modified 6 months ago • written 6 months ago by Jennifer Hillman Jackson ♦ 25k

Admin update: VCF data displays correctly now. All of the related issues were resolved in July.

ADD REPLY • link written 3 months ago by Jennifer Hillman Jackson ♦ 25k

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