Question: UCSC genome viewer for non-model organism
0
gravatar for anu014
18 months ago by
anu014160
India
anu014160 wrote:

Hello all,

I've done chip-seq analysis with macs2 & got bed & bedgraph files for peaks. My organism is mycobacterium tuberculosis & I cannot find the organism on UCSC browser. How to visualise the files now? Please help me out.

Thank you in advance :)

ADD COMMENTlink modified 18 months ago by Pierre Lindenbaum115k • written 18 months ago by anu014160
3
gravatar for Pierre Lindenbaum
18 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum115k wrote:

create a custom Genome Browser Track Hubs https://genome.ucsc.edu/goldenpath/help/hgTrackHubHelp.html

Track hubs are web-accessible directories of genomic data that can be viewed on the UCSC Genome Browser (please note that hosting hub files on HTTP tends to work even better than FTP and local hubs can be displayed on GBiB). Track hubs can be displayed on genomes that UCSC directly supports, or on your own sequence. Hubs are a useful tool for visualizing a large number of genome-wide data sets. For example, a project that has produced several wiggle plots of data can use the hub utility to organize the tracks into composite and super-tracks, making it possible to show the data for a large collection of tissues and experimental conditions in a visually elegant way, similar to how the ENCODE native data tracks are displayed in the browser.

see also this (OLD) post : http://plindenbaum.blogspot.fr/2013/07/playing-with-ucsc-genome-browser-track.html

ADD COMMENTlink written 18 months ago by Pierre Lindenbaum115k
1

anupriyaverma1408 : You should check out UCSC MIcrobial genome browser. Here is one for Mycobacterium and then use a custom track or @Pierre's suggestion.

ADD REPLYlink modified 18 months ago • written 18 months ago by genomax59k

Thanks Pierre & Genomax.

Custom tracks creation was not needed right now as the required organism was already present on http://microbes.ucsc.edu. So I simply uploaded the bedgraph files from macs2 as discussed here: Visualising BedGraph files on UCSC [custom tracks]

Thanks for this blog, seems useful for my next organism: http://plindenbaum.blogspot.in/2013/07/playing-with-ucsc-genome-browser-track.html

ADD REPLYlink written 17 months ago by anu014160
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