Download source code from dropbox.
This code release fixed a bug associated with SAM track display. When displaying read alignment data during genomic juxtaposition mode, the track image appeared to be shifted due to the bug, now it's fixed.
Besides, you can now drag on any of the genome annotation tracks to scroll.
Try this link to open the browser and show the tracks as displayed in the screen shot below:
http://epigenomegateway.wustl.edu/browser/?genome=hg19&juxtapose=LTR&gftk=LTR,full&coordinate=chr1:1340000-1390000&custombam=stat1hela,http://vizhub.wustl.edu/hubSample/hg19/sam1.gz,thin
As illustrated in this example, genomic juxtaposition focuses the view on LTR elements and reveals that STAT1 ChIP-Seq reads bind one LTR copy, suggesting this LTR copy has something to do with STAT1's business in HeLa cells.
STAT1 ChIP-Seq data comes from this publication: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
This code release fixed a bug associated with SAM track display. When displaying read alignment data during genomic juxtaposition mode, the track image appeared to be shifted due to the bug, now it's fixed.
Besides, you can now drag on any of the genome annotation tracks to scroll.
Try this link to open the browser and show the tracks as displayed in the screen shot below:
http://epigenomegateway.wustl.edu/browser/?genome=hg19&juxtapose=LTR&gftk=LTR,full&coordinate=chr1:1340000-1390000&custombam=stat1hela,http://vizhub.wustl.edu/hubSample/hg19/sam1.gz,thin
As illustrated in this example, genomic juxtaposition focuses the view on LTR elements and reveals that STAT1 ChIP-Seq reads bind one LTR copy, suggesting this LTR copy has something to do with STAT1's business in HeLa cells.
STAT1 ChIP-Seq data comes from this publication: Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
Hi, I'm writing to report a broken link in the User Manual for the browser.
ReplyDeleteThe link is supposed to be on the chapter for 'gene plots'. It is found at the bottom of this page
http://epigenomegateway.wustl.edu/browser/manual/#g-b-b
The link seems to point to a local installation of the browser:
http://localhost/browser/manual#g-b-b
Thanks,
Shraddha Pai
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Shraddha Pai, Ph.D.
Post-doctoral fellow
Krembil Family Epigenetic Research Laboratory (Lab head: Dr. Art Petronis)
Centre for Addiction and Mental Health, Toronto
Sorry about the broken link. It points to a manual page that has been removed.
ReplyDeleteFor the moment, please visit this link which shows some of the configuration options that are currently available.
http://epigenomegateway.wustl.edu/browser/manual/#g