Wednesday, April 9, 2014

v37: More options and bug fixes

If you're upgrading from previous version, you need to re-compile "subtleKnife.c". This version has many changes listed below:

1. App finder. Go to Apps and use the text box to find apps:

You may be interested to look for these hidden apps: Metadata term finder, Sequence fetcher, Datahub validator.

2. Validate datahub. Search by "hub" or "validate" to find this app:

This is a preliminary version of hub validator, and is capable of validating tracks (if there's no JSON errors anywhere in the hub). It won't add or register custom tracks in the hub. It is expected the hub to be of same reference genome as the one the browser is running on.

3. Better handling of broken tracks. Previously only numerical tracks can be handled.

4. Correct SVG color coding, solved an error when there's transparency involved. Thanks to Kamil Slowikowski!

5. CHG methylation. In methylC track, when you combine cytosine methylation level from two strands, only CG cytosines are combined, but not CHG cytosines since they are highly asymmetrical in mammalian genomes. But now we give user the option to combine that, by checking an additional checkbox:

Combining CHG (CAG/CTG) methylation data is desirable in certain cases (strong symmetry of CHG methylation in the plant genomes). This option will only appear when there's strand-specific CHG data present in a methylC track. We thank our anonymous reviewer for helpful discussions and suggestion of this feature.