Sam Gardner's profile - activity

If you checked the option for "Don't ask about this genome again" for one or more genome assemblies, but would now like GenomeBrowse to prompt you to download reference sequence for those assemblies again, please try the following:

1) Choose "Options..." from the "Tools" menu (or click the gear in the toolbar).

2) On the "General" tab look for the "Reset Message Suppression" button in the center. Click it.

3) Then either close and re-open GenomeBrowse, or change the genome assembly (using the drop-down list in the toolbar).

Note: Step 3 assumes GenomeBrowse's default behavior of saving settings on close.

Also note: The correct reference sequence can be downloaded through the Add dialog. It is not necessary to get the prompt.

I hope that helps, if it was something else you wanted to know how to reset, or if you have are any further questions, don't hesitate to ask.

I think I can make this work. I'm currently developing a solution, while addressing some other location bar parsing concerns.

The change should make it into the next GenomeBrowse release which is planned for later this week.

My tentative solution would allow the chromosome, start, and stop sections of the coordinate entry to be separated by any white space (such as the tabs in your example).

As long as all goes well, it should handle text formatted like any of the examples below:

1 10 20
1:10-20
1:10:20
1-10-20
1 10 - 20
1 : 10 - 20
chr1 10 20
chr1:10-20
chr1:10:20
chr1-10-20
chr1 - 10 20
chr1 - 10 : 20

This might mean that it can't handle something like:

chr 1 : 10 - 20

but, we will see.

Thanks for the suggested improvement.

To expand on Jami's answer, although it's very enterprising to convert a BED file to BAM, the files have very different focuses on the types of data they support and the experience of viewing the converted data would be approximate at best.

Similarly, FASTA or GFF would not convert well to BAM. As Jami mentioned though, we plan on building built in support for converting all of these file types in the future.

For the moment, we are "bootstrapping" GenomeBrowse with the technology of SVS. This means for viewing annotation sources GenomeBrowse relies on annotations being converted to our efficient binary IDF file format.

SVS produces IDF files when converting BED, FASTA, GTF or any text file downloaded from the UCSC genome browser table viewer. GenomeBrowse is set up to auto-detect files that SVS converts, and they are ready to plot the next time you go to the Add dialog.

SVS is Golden Helix’s analysis product for a variety of workflows and is a commercial tool, you can request an evaluation of SVS through the evaluation request form.

There are, of course, many ways such a thing could be accomplished. The simplest way I can think of at the moment, would be to utilize a future feature. We are already planning to implement some variation of user defined 'bookmarks' in genomic space. These would be organizable to some extent and exportable in one or more formats which may be useful elsewhere. Once that feature has been implemented, we could conceivably write a script for SVS to read the exported 'bookmark' list (your flagged variant list, in this case) and mask all intersections in one or more spreadsheets of your choosing.

In short, your procedure would be:

1. Mark variants in GenomeBrowse
2. Export the marked variant list
3. Run the masking tool in SVS
4. Run analyses on the masked data