Oncorhynchus mykiss (Rainbow trout) genome request

[Jeff Strohm]

Hi Jim,

The salmon genome that you kindly hosted for us last week is a huge hit with our working group!

Are you able to host the rainbow trout for us as well? Here's the location of fasta and annotation downloads: http://www.genoscope.cns.fr/trout/data/

Many thanks!

-Jeff

[James Robinson]

Hi Jeff,

Yes, I’ll put it on my list. 

Jim

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[James Robinson]

Hi Jeff,

I took a quick look at the files.  There are some problems with the annotation files,  they are not correct GFF format.  In particular, column 9.   The consequence is that constituent gene parts  (CDS, utr, etc)  can’t be aggregated into features, so every row appears as a unique un-named feature in the visualizer.    Any chance that the lab could fix the annotation files?

Jim

On Mar 11, 2016, at 10:12 AM, Jeff Strohm <strohm...@gmail.com> wrote:

[Jim Robinson]

I added this genome, but it only includes the "Gene" records from the annotation files.   If the annotation files are properly formatted as gff, preferably gff version 3,  reply to this message and I will see if I can do an update. 

Also, a note, the files are not gzipped despite having a "gz" extension.  If you download and try to load them be aware of that, you need to remove the ".gz" extension.

[Jeff Strohm]

Thanks Jim! I'll see what I can come up with Re: file formats... for now just the Gene features should suit our needs.

I realize IGV is geared towards visualizations, but I'm curious if you have advice on the analysis we are attempting.

We have three different microarrays and we have mapped the ESTs from them onto the S. salar genome using HISAT2. We can visualize all of the info we need on a small scale, i.e. where the ESTs from the different arrays align/ overlap at the same region, and the gene/ feature at that region.

But since we have ~100,000 ESTs we need a way to output this info in an automated manner. Again, we are looking for an output file that contains which ESTs overlapped, the chromosome location, and the gene/ feature at that location.

I believe we have all of the components, but I'm not sure where to go next.

Thanks!

-Jeff

[Jim Robinson]

I think a good starting point for that type of analysis would be BedTools  http://bedtools.readthedocs.org/en/latest/.

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