Tag Archives: coge

Genes (RNA-Seq) on Oly Genome

We currently have a version (0.0.2) of the Ostrea lurida genome on CoGe. This is 38 scaffolds greater than 80k bp. Below is an effort to map gonad RNA-seq data to said genome.

Two male gonad and two female libraries were mapped to the genome using TopHat in Cyverse Discovery Environment.
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Through the steps…

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I moved the data in Discovery Environment to coge_data directory.

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Will see what Expression Analysis does…

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Some output

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This created two files and corresponding tracks: read depth and BAM alignment

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Will crank out other three libraries and soon will work on rough annotation.

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Getting back on tracks

Yesterday I uploaded v0.0.1 of the Geoduck genome to CoGe.

Now I want to start adding tracks. To do this I used CLC to create RNA-seq tracks from our male and female gonad transcriptome data.

As would be expected only a small amount of reads mapped. This is as we are limiting the genome to the 22 scaffolds with length > 100k.

Males
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Females
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One thing to point out (and will have to be followed up on) is that many more Female reads mapped back.

I took the Reads data and exported to BAM.
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Then uploaded to CoGe.
I called this Version 1, and interestingly I got some cool options.. so I selected them.

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This included saving as a Notebook.

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This was Finished in less than 5 minutes!
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The SNP view.
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Voila – we have it in a Browser.
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and you can zoom in
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Here we have a Notebook view
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It is now public, though not quite sure if there is a url.

Everything is public so please give it a look / twirl.
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Panoplea of data

We have had the data for a draft genome of Panopea generosa for a bit. Here is a quick look.

All raw data is available @ http://owl.fish.washington.edu/nightingales/P_generosa/

With a first pass assembly here.

There are over 14 million scaffolds at this point with 22 scaffolds greater than 100,000 bp. We are using those to kick the tire of COGE and see if this is good portal for analysis and sharing.

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There is not much to see now in the genome browser, but should hopefully have more soon.
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