bed file

[thomasyu888]

Hello,

Thanks in advance for your time. I was wondering if I was doing something wrong configuring the bed file. This is my source configuration:

{name: 'example_bed',
collapseSuperGroups:true,
uri: 'http://localhost/example.bed.gz',
tier_type: 'tabix',
payload: 'BED'}

This is the bed file I bgzipped and created a tabix index file on it.

chr7 127471196 127472363 chr7 127472363 127473530 chr7 127473530 127474697 chr7 127474697 127475864 chr7 127475864 127477031 chr7 127477031 127478198 chr7 127478198 127479365 chr7 127479365 127480532 chr7 127480532 127481699

Please kindly let me know what I'm doing wrong.

Tom

[dasmoth]

The "payload" names are case sensitive. Could you try:

        payload: 'bed'

instead.

Will leave this open until I have a chance to look into an error-handling issue this reveals...

[thomasyu888]

Thank you for your help. I changed the payload to lowercase, but it still doesn't seem to want to display anything. Attached is a screenshot.

[ajo2995]

Try another chromosome. I am seeing a bit g where the first contig ( I my case ) is not working for tabix indexed bed files Andrew

On Sep 14, 2015, at 6:42 PM, Thomas Yu notifications@github.com wrote:

Thank you for your help. I changed the payload to lowercase, but it still doesn't seem to want to display anything. Attached is a screenshot.

— Reply to this email directly or view it on GitHub.

[dasmoth]

@ajo2995 that sounds as though some lines from your file have been interpreted as header data when making the Tabix index. Do you have a file I could try?

[dasmoth]

Okay, found a bug which quite likely explains this and also @ajo2995's problem. Solution implemented on the 'master' branch (although not currently in the release).

Do re-open if you're still having problems.

[ajo2995]

That fixed it. Thanks!

[thomasyu888]

Thank you for your help. This seems to work if I have a bed file that includes all the chromosomes. However, when I just put the above bed file in, it seems to only plot the first line.

[dasmoth]

That's very odd and doesn't match the results of my own testing using the file you sent. Any chance you could send me your .bed.gz and tabix files for that (via offline e-mail probably best).