Markus Riester

Read10X_Image: Support for SpaceRanger 1.1 aggregate function

3

Hi, Latest SpaceRanger 1.1 comes with a new aggregate function to merge multiple slides. In Read10X_Image, "tissue_positions_list.csv" is currently hardcoded. For aggregate, it's called "aggr_tissue_positions_list.csv", located in the parent directory...

Output generated by versions using 3.6+ are not readable by 3.5 or older. We should set a version explicitly and make it a command line option.

Fixed basis example

2

Hi, I'm struggling with fixing a basis. NMF tells me that the basis was not fixed and the method might not support it. But it I cannot get any method...

Headers then lack the contig and gatk stops because of different contigs in input files.

Important for example for prostate cancer AR amplifications.

Calling homozygous deletions should be accompanied by a double check of SNPs in the segment. If not balanced, then flag. If no SNPs, flag unless high likelihood of deleted.

Obsolete in Bioc. ASCAT has a good replacement function, needs some work to incorporate.

Hi, I had to make a few changes to make it run locally within our organization. My Perl is a bit rusty, so I didn't do a pull request, but...

Currently always return PDF, but optionally PNG. Change to specify it directly, with default of PNG because PDFs get huge with HD. --image_format=pdf:png