Missing config.yaml Reference Files in Documentation, Analyses about microexonator HOT 3 CLOSED

Hello cburghard,

Indeed, the analysis does depend on the annotation files you provide at the config.yaml. I will improve the documentation in the README file to clarify a bit more about the origin of these files.

ME_DB correspond to an optional file, but it could help to enhance the detection rates of microexons that are already annotated. Getting the bed12 files from VAST DB might be quite elusive, so I will try to find a way to provide an easier solution, but at least the way I am getting these files is by connecting to their UCSC hub (http://vastdb.crg.eu/tracks/VastDBhub/hub.txt). You can do this by inserting their hub link at https://genome.ucsc.edu/cgi-bin/hgHubConnect and then you can use the Table Browser to retrieve their track as bed12 files. MicroExonator scans for microexons that are annotated on these files, but I am also planning to enable the users to input standard bed files that can directly indicate microexon coordinates.

Regarding the link to the UCSC table browser, I did not intend to set Gencode basic v19 as the default value for the link, I think these are the default values that everybody gets when accessing the Table Browser. I recommend you to use the most comprehensive annotation available for the genome assembly of your interest. Using the most complete gene annotation possible will enable MicroExonator to interrogate more splice junctions to find novel microexons, so GENCODE comprehensive would be better than basic. In fact, I have been using the GENCODE comprehensive for all the analysis done in mouse and human.

Thanks for the feedback and please let me know if you have other questions or issues.

from microexonator.

These issues are now addressed on the new documentation:
https://microexonator.readthedocs.io/en/latest/discovery_and_quantification.html

Thanks a lot for your feedback.

from microexonator.