Error in dcast.data.table(data = celltagCounts, formula = Cell.BC ~ Cell.Tag, : Can not cast an empty data.table about biddyetalworkflow HOT 4 CLOSED

this error occured at the Rscript ./scripts/matrix.count.celltags.R ./cell.barcodes/hf1.d15.barcodes.tsv v1.celltag.parsed.tsv hf1.d15.v1

from biddyetalworkflow.

Hi @skyou123,

This error is probably caused by an issue with your input files for the script, specifically the file v1.celltag.parsed.tsv. Can you try regenerating the v1.celltag.parsed.tsv file and try again? If you still get this error it would be helpful if you could share the commands you used to create the v1.celltag.parsed.tsv file as well as the file itself.

Thanks,
Brent

from biddyetalworkflow.

Hi Brent Biddy,

I tried regenerating the  v1.celltag.parsed.tsv  file and it did not work.
Though, I changed you code in celltag.parse.reads.10x.sh, in line 36,  to "match($10, /GGT(.*)GAATTC/, celltag);", and it works.

In the end, I completed the pipeline in CellTagWorkflow, thanks for your reply!

Best

Zhiwen You
institute of neuroscience(ION), Chinese Academy of Science(CAS)

from biddyetalworkflow.

Hi Zhiwen,

Thank you for posting your fix. I am glad you were able to complete the workflow. While I can't be positive, based on the fix you posted, I am guessing the error you experienced was a result of not including parentheses around [ACTG]{8} in the tagregex option for the celltag.parse.reads.10x.sh script.

Like so: -v tagregex="CCGGT([ACTG]{8})GAATTC"

It is necesarry to include these parentheses in the CellTag "motif" when using this script. I just wanted to mention this in case anyone else experiences a similar error.

Best,
Brent

from biddyetalworkflow.