uploading bam files

[Jerry Mersel]

Hi:

    I am a sys admin given the task of upkeep of our ucsc genome browser. Recently I received some questions and requests from a user.

The user wants to upload some bam files. I want to place  the bam files under a directory under /gbdb and then create a link to the particular directory under goldenpath so that the bam files can be accessed by the user. Is this an acceptable method? The user can then update custom tracks by accessing that particular URL.

Is this correct?

The user also wants to add a barley genome to the database. 

What are the steps to do this.

Thank you for your help.

Jerry

[Brian Lee]

Quote Edit Delete

Dear Jerry,

Thank you for using the UCSC Genome Browser and your question about approaches to control your genome browser mirror to help supply custom data.

One of our engineers shares that for the question of placing a bam file in the /gbdb/ directory you can edit a hg.conf setting to allow for a location of these files. If you change the setting in hg.conf to the following:

udc.localDir=/gbdb/hubs

You would be able to then host data in that location and have a custom track line like:

track name="my gtexSignal" type=bigWig bigDataUrl=/gbdb/hubs/gtex/hg38/wholeBlood/gtexRnaSignalSRR820779.hg38.bigWig

The custom track tool will find it as long as the location starts with "/gbdb/hubs/".

For your barley genome approach you could use an Assembly Hub, which is a way to attach new genomes:
http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly

You may also want to look in our archives for histories of correspondence with users who have loaded assemblies on their mirror. In fact our archives are the best place to start for all your questions as often in our mailing list responses we may not think to share all possible information that could be of help:
https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome-mirror/assembly
https://groups.google.com/a/soe.ucsc.edu/forum/?hl=en&fromgroups#!searchin/genome/assembly$20hub

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. Or there is also our other non-mirror specific mailing list gen...@soe.ucsc.edu. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UC Santa Cruz Genomics Institute

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To post to this group, send email to gen...@soe.ucsc.edu.
Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAPusz98Trn-QztOC3h-XCyi3hub3FJyPHyC0uidVOPsyGQiXOQ%40mail.gmail.com.
For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.

[Jerry Mersel]

thanks!

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CAKy8-o5VHthhJJ5RZfhqa_Lav7b1V%3D-1f4ziYgaNdeBJqyiDug%40mail.gmail.com.