CellTagPostCollapsing returns collapsed.count with 1 row when reading in multiple BAM files

[bc2zb]

Hello, I've run the pipeline on a number of bam files going from 1 to 3, and whenever I attempt to run the pipeline on more than one bam file, CellTagPostCollapsing assigns a collapsed.count slot with 1 row. During the run of CellTagPostCollapsing. I can run the pipeline on my individual bam files without issue, but when I try to include multiple, I run into this. I think that the aggregate function call is missing during the step that combines the results of starcode together, as this warning pops up.

Aggregate function missing, defaulting to 'length'

I'm not a data.table expert, and I've not tried to tear apart the source yet, but will add on if I figure out anything.

[KaetheKong]

Hello, Thank you for using the tool!

First of all, we have significantly modified our pipeline recently. Please make sure the package is up-to-date. We haven't changed the version number yet. Maybe consider reinstalling with force rewrite.

Additionally, would you mind providing us more details regarding the error/issue? For instance, which commands were used? And how are the files/filenames organized, like for the collapsing files and the collapsing result files? And would you mind sharing a part of your pre.starcode slot in the object? Maybe we can start from there!

And also check this issue, it might be helpful! - https://github.com/morris-lab/CellTagR/issues/4

Best, Wenjun

[bc2zb]

system("~/starcode/starcode -s --print-clusters _Sample-1.txt > collapsing_result_Sample-1.txt") system("~/starcode/starcode -s --print-clusters _Sample-2.txt > collapsing_result_Sample-2.txt") system("~/starcode/starcode -s --print-clusters _Sample-3.txt > collapsing_result_Sample-3.txt")

I solved it, initially, I had prefixed sample id to the beginning.