.2bit has been added.
Features file is added and needs testing.
HEADER.md for non-UCSC

Features look good in IGB.
Added README.md

Removed README.md should be HEADER.md

Field14 not detected in IGB. Working solution.

Sorting is causing an issue with IGB detecting field14 in the BED file.

FILES attached —
Sorting the bed file by protocol (-k1,1 -k2,2n) is causing a formatting error between lines 1-14 and 15 - 6160. This is preventing IGB from displaying field 14 (See IGB view Std Out). Two tab spaces are required from lines 15 - 6160 to resolve the issue. I need to add an additional tab space after field1 of each line from 15-6160.

If the extra tab space is added - IGB functions as expected. See IGB view Reformatted.

Sublime shows single tab space between field1&2 (lines15-end) but IGB is interpreting the tab as just a space. Replacing the whitespace between fields1&2 with space OR tab aligns the fields the same. There might be something with how IGB is interpreting that space therefore how it's displaying field14.

If two tab spaces between fields 1&2 are used to align lines 15-6160 to 1-14, IGB correctly displays description.

Do I need to do something for this issue? The bed file seems to be working on my system, field 14 is showing correctly.

I just wanted to bring it to your attention that I reached that point. Out of curiosity, did you drag and drop the bed file or reformatted file into IGB? There is a file that I reformatted a few lines of to show that it works in that format. Otherwise, I attached the screen shot of how the 'typical' bed file would look in IGB for me.

Resolved, thanks to Nolan! The annots.xml file was pointing to the GFF file and not the BED file - no corrective formatting required.

Files in Dropbox folder don't reflect comments below.

• annots.xml references C_albicans_WO-1_Jul_2010_refGene.bed.gz, which is not there
• refGene should only be used for annotations obtained from UCSC database
• there is a README.md file but no HEADER.md file

• This issue is for the Dec 2013 assembly. The annots points to C_albicans_WO-1_Dec_2013.bed.gz
• I show no _refgene uses in this directory
• Other (C_albicans) assemblies only have README.md files. Should all assemblies have HEADER.md?

Still to do:

• Add HEADER.md summarizing where the files added to QL came from.

Committed all files (except still-to-be-created HEADER.md file) to SVN repo.