cschmidl

Hello! Is it possible to find DARs of a set of clusters versus all others (e.g. merge cells in clusters 1,2,3 and search for DARs agains cluster 4-10)? Thank you...

Hello! Is it possible to extract reads from a specific cluster to a bamfile so I can treat it as a "pseudo bulk" sample? Thanks a lot for your help!

Annotation of additional data to single barcodes/cells

1

Dear Rongxin, can I add additional metadata to 1) single barcodes/cells or 2)even only to whole experiments during "createSnap"? Concerning 1 I want to add protein-expression values and then visualize...

After macs2 sambamba is called as defined in atacseq.yaml, but the nex sambamba view command is simply calling "sambamba": macs2 callpeak -t .... sambamba-0.7.1 depth region -t .... sambamba view...

ATAC-seq pipeline exit if no mitochondrial reads are duplicated

3

ATAC-seq pipeline exit if no mitochondrial reads are duplicated due to zero division error - see logfile: File "/Users/christianschmidl/src/open_pipelines/pipelines/atacseq.py", line 359, in parse_duplicate_stats prefix + "duplicate_percentage": (float(duplicates) / (single_ends +...