UCSC for Arabidopsis?

[BioTalk]

Hello All,

Would it be possible to load arabidopsis genome in UCSC browser? If yes, how? Please help!

Thank you,

[malachig]

UCLA hosts a mirror of the UCSC Genome Browser that has been augmented with A. thaliana. Apparently this is an ongoing collaboration with the Jacobsen lab. Link follows:
A. Thaliana Genome Browser

[BioTalk]

Thank you for you help. Do you know how to load you own data along with this data to UCSC browser?

I would like to see the expression of the regions with respect to reference genome. Would that be possible?

Thank you,

[malachig]

You should be able to load your own data as a 'custom track' in this browser as you would in any other instance of the UCSC browser. There are several ways to do this, including manually uploading a file or placing it in a web accessible directory and crafting a URL to load the file from that location. There are also several data/file formats available for custom UCSC tracks (wig, bigWig, GFF, GTF, BED, etc.).

All of this is explained here:
UCSC custom tracks
Wiggle format
BigWig format

You can see an example of expression data being displayed as custom tracks at the following link. Open the 'Data links ...' section and click on one of the links there ('C' or 'P'). I crafted the URLs on these pages so that they load a custom track file and take you to a specified gene region in the human genome.
Example usage for custom UCSC tracks

Another option is to get your A. thaliana annotations into IGV and view your RNA-seq expression data there. IGV supports various file formats for viewing annotation and sequence data:
Download IGV
Supported file formats

[kmcarr]

UCLA hosts a mirror of the UCSC Genome Browser that has been augmented with A. thaliana. Apparently this is an ongoing collaboration with the Jacobsen lab. Link follows:
A. Thaliana Genome Browser

One caveat about that site is that the version of the Arabidopsis genome is fairly old, TAIRv7. In fact all of the genomes there appear to be old (human is hg17). Be careful if your tracks were derived from alignment to a different build of the genome.

[chris]

The Ensembl Genomes project has expanded the Ensembl browser to use many more genomes. For Arabidopsis see here:

http://plants.ensembl.org

It works similarly to the UCSC browser, but includes the up-to-date TAIR9 build.

[BioTalk]

Thanks so much all for your help. I think Ensemble will work for me as it is based on TAIR9.

Thank you all!

[BioTalk]

You should be able to load your own data as a 'custom track' in this browser as you would in any other instance of the UCSC browser. There are several ways to do this, including manually uploading a file or placing it in a web accessible directory and crafting a URL to load the file from that location. There are also several data/file formats available for custom UCSC tracks (wig, bigWig, GFF, GTF, BED, etc.).

All of this is explained here:
UCSC custom tracks
Wiggle format
BigWig format

You can see an example of expression data being displayed as custom tracks at the following link. Open the 'Data links ...' section and click on one of the links there ('C' or 'P'). I crafted the URLs on these pages so that they load a custom track file and take you to a specified gene region in the human genome.
Example usage for custom UCSC tracks

Another option is to get your A. thaliana annotations into IGV and view your RNA-seq expression data there. IGV supports various file formats for viewing annotation and sequence data:
Download IGV
Supported file formats

What data formate do you think we need to give into IGV in case if we wants to see sequence expression?

[malachig]

Many people use the Wig or BigWig formats to display expression data on a base-by-base level. In the following example, the last three tracks are in Wig format:

Example of custom UCSC tracks

Wig files will also display in IGV.

[BioTalk]

Many people use the Wig or BigWig formats to display expression data on a base-by-base level. In the following example, the last three tracks are in Wig format:

Example of custom UCSC tracks

Wig files will also display in IGV.

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18&position=chr19:56153600-56164841&hgt.customText=http://www.alexaplatform.org/alexa_seq/5FU/ucsc/DE/HS04391/HS04401_vs_HS04391/chr19_24_DE_merged.txt.gz&ctfile_hg18=

That means grey scale linings (of atickleback, x-tropicalis and chicken) were from .wig file?

Would that be possible to see bar graph similar to track HS04391_n1 and hs04401_n1?

[malachig]

The conservation track at the top is provided directly by UCSC, so I don't know the details of how it is constructed. The 'HS04391_n1 and hs04401_n1' are already bar graphs... Each 'bar' is only one base position wide. Perhaps you want each bar to represent a bin of data?

You can customize the display of these tracks by clicking the bar on the left hand side of each track. For example, you can change it from 'bar' to 'points'. You can also apply a smoothing function.

If you want the data to be summarized over windows (instead of base-by-base) to get more of a 'bar' look, you can adjust the way the wig file is created:
Wig format