Genome Browser "No Data" Error
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Robert Amezquita
Jul 26, 2016, 11:39:32 AM7/26/16
to gen...@soe.ucsc.edu
Hi,
I am trying to get my trackhub to work, however, all the tracks show up as "No data". I've tested these tracks in IGV, and they do show indeed show to have data as they work there. Additionally, I copied over my settings from a previous hub that was working and is loading fine, so I'm not sure what the error is..
These bigwigs were generated using deeptools2 bamCoverage. The hub is located at:
Thanks for your help in advance...
-Rob
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Robert A. Amezquita
HHMI Gilliam Fellow | Canaan-Yale Fellow
PhD Candidate | Kleinstein & Kaech Labs
Yale University | Department of Immunobiology
300 George St, Suite 505
New Haven, CT 06511-6663
Cath Tyner
Jul 26, 2016, 8:00:16 PM7/26/16
to Robert Amezquita, UCSC Genome Browser Public Help Forum
Hello Rob,
Thank you for using the UCSC Genome Browser and for submitting your question regarding issues with your track hub not displaying expected data.
Thank you for using the UCSC Genome Browser and for submitting your question regarding issues with your track hub not displaying expected data.
It appears that formatting may be causing the problem. In the example lines below, "1" is being used to represent chromosome 1. Please try using "chr1" instead, which should fix the problem.
File from hub:
http://128.36.40.203/ucsc/Hub3/mm10/trackDb.txt
File: http://128.36.40.203/ucsc/Hub3/mm10/bigwig/ATAC_Blimp1KO.MP_d10/Sample_SG_63_002.bw
bigWigToWig Sample_SG_63_002.bw out.wig
[brianlee@hgwdev moreJunk]$ head out.wig
#bedGraph section 1:0-4189599
1 0 3010470 0
1 3010470 3010480 2.92
1 3010480 3010490 5.83
1 3010490 3010600 8.75
1 3010600 3010610 9.72
1 3010610 3010620 13.61
g
ing to:chr
1 3010610 3010620 13.61Please let us know if that solution does not work for you so that we can help you troubleshoot further.
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Cath Tyner
Jul 27, 2016, 7:22:11 PM7/27/16
to Robert Amezquita, UCSC Genome Browser Public Help Forum
Hi again Rob,
To assist you with your goal, you can review this similar previously answered question:
Ensembl uses chromosome names of "1" where UCSC uses: "chr1"
You need to convert the Ensembl chromosome names to the UCSC names. The sed command: sed -e 's/^\([0-9XY][0-9]*\)/chr\1/; s/^MT/chrM/;' converts names in column one of a file from Ensembl to UCSC names.
On Tue, Jul 26, 2016 at 5:47 PM, Robert Amezquita <robert.a...@yale.edu> wrote:
Crud! I knew that. Thanks for your help. Is there any utility to add "chr" to the chromosomes directly to the bigwigs? (Or enable using the Ensemble reference with just the numbers?)
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