Aaron Quinlan
Aaron Quinlan
Hi Kathleen, This is an error being raised by pysam and it seems to be indicating that a chromosome label in one of the alignments is not found in the...
Not sure, what do the chromosome labels for your alignments look like: ``` samtools view kathleen.bam | cut -f 1 | sort | uniq -c ```
Okay, thanks for the update. It looks like `count-errors.py` expects sequence names to have at least 5 "_" separated components. Based on your commands above, it looks like you have...
Hey Brent, One of the issues we are seeing with interpreting putative SVs is the lack of simple repeat and microsatellite tracks. Is this something that would be easy to...
"Hey this is a cool project. In the figure you show species as the top level directory but the recipes aren't following that scheme currently?" I absolutely agree. It is...
Thanks all, I will try to incorporate fixes for this and another outstanding bug soon. I have been horribly bogged down with other deadlines. Thanks for the patience.
I just pushed a change that should address these issues.
Thanks so much for all of these changes. I have been swamped with other work, but will get back to integrating all of this when I return from vacation in...
I added a LICENSE file and updated the banners to reflect MIT license.
Interesting idea. The main challenge here is that in order to make each line have the same number of columns, one must do a full scan of the input to...