Getting back on tracks

Posted by & filed under Panopea generosa.

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
CLC_Genomics_Workbench_8_5_1_1CAD8B6E.png

Females
CLC_Genomics_Workbench_8_5_1_1CAD8BCB.png

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.
CLC_Genomics_Workbench_8_5_1_1CAD8C40.png

Then uploaded to CoGe.
I called this Version 1, and interestingly I got some cool options.. so I selected them.

CoGe__My_Data_1CAD8C90.png

This included saving as a Notebook.

CoGe__My_Data_1CAD8CC2.png

This was Finished in less than 5 minutes!
CoGe__My_Data_1CAD8CEB.png

The SNP view.
CoGe__My_Data_1CAD8D42.png

Voila – we have it in a Browser.
JBrowse_scaffold860_1__221360_and_Getting_back_on_track_md_1CAD9095.png

and you can zoom in
JBrowse_scaffold4546_56623__57472_1CAD8E29.png

Here we have a Notebook view
CoGe__My_Data_1CAD8E81.png
It is now public, though not quite sure if there is a url.

Everything is public so please give it a look / twirl.
CoGe__My_Data_1CAD8F10.png

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