To show these in IGB:

• Create files that IGB can read (e.g., BED4 format)

The regions are probably simple spans with chromosome name, start, and end position, and maybe a strand indicator. When users select and load data from the file with blacklist regions, they should see the name of the region displayed.

Please use genome_src repository to place code used for this.

[~aloraine] - do we want to store the files in IGB Quickload?

Replying to previous comment: Yes, alongside gene annotations. When you commit to svn, please include ticket number in the commit message (for future reference).

I have been unable to identify specific patch versions for the blacklist genomes. There is a file for each genome with metadata, but it only lists the assembly without the patch information. From reading this description on patches, they do not affect chromosome coordinates, so the patch version should not have any effect on the blacklist regions.

Heads up in case you are on Mac and update to Big Sur, SVN is not officially supported but can be installed through HomeBrew.

https://developer.apple.com/forums/thread/666689

[~aloraine] - I think I found a discrepancy in the naming of one of the Drosophila genomes.

UCSC lists the Drosophila Aug. 2014 assembly as dm6.
igbquickload.org/quickload has D_melanogaster_Jul_2014 as a genome version.
Synonyms.txt lists D_melanogaster_Aug_2014 as being the dm6 assembly.

Looking at the flybase site, it is unclear precisely what date is correct. NCBI lists the same date of release (August 2014) as UCSC for dm6. NCBI states that "The gene annotation is based on Release 6.32 provided by FlyBase." The file in igbquickload.org is 6.03.

Any thoughts on this would be appreciated. I would assume that various versions of dm6 contain the same chromosome coordinates, so the blacklist should be applicable to any version of dm6. I could add the blacklist file to D_melanogaster_Jul_2014. We may want to then update the synonyms.txt to point to D_melanogaster_Jul_2014 for dm6, so that the UCSC data can also be loaded.

After reviewing the dm6 issue with Dr. Loraine, I have created a new ticket (IGBF-2952) to address the issue.

Wait to push the dm6 blacklist until IGBF-2952 is complete.

All of the blacklist files have been pushed to the SVN repository, with the exception of dm6.

I have created IGBF-2955 to address pushing the changes to the SciDas and Quickload servers.

Please don't test until sites are updated and deployed. (Sorry - I moved this forward to "ready for testing" prematurely.)

Now it is ready for testing.
attn: Nowlan Freese

Discrepancy - While testing I noticed that in the C_elegans_oct_2010 (ce10) genome the blacklist region was outside of the range of some of the chromosomes (i.e. the blacklist regions were greater than the max chromosome size). The genome length in IGB (C_elegans_oct_2010) is correct when compared to UCSC. I also re-downloaded the ce10 blacklist file. It appears that the locations of some of the blacklist regions are incorrect or mis-annotated, indicating an issue with the pipeline that the blacklist authors used.

Testing complete, no issues.

Closing ticket.