Dear Chen,

Thanks again for making this wonderful tool and pipeline available. I have run the redeemV pipeline smoothly and get all expected results. One issue I have, however, is that I have multiple 10x multiome reactions. Thus, after running the pipeline, have multiple QualifiedTotalCts and RawGenotypes files from each run. Correct me if I am wrong, but I don't think I can simply concatenate the files because of the potential shared barcodes from different cells from different 10x reactions. I wonder if you could provide some guidance on where and how to modify the redeemV output files from different reactions so that they can be combined/pooled for the downstream redeemR analysis.

Thank you,
Li

Hi,
I'm running redeemV on 10x scRNA/ATAC from human but I get this error and files are empty.
what could be the issue?

rror in read.table(RawGenotypesFile) : no lines available in input Execution halted Traceback (most recent call last): File "/home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Software/bulkWGS/Sadeghi/redeemV/REDEEM-V/mitoConsensus//RemoveStrandBias.py", line 16, in <module> with open(StrandBiaseBlackList_file) as f: FileNotFoundError: [Errno 2] No such file or directory: '/home/i439h/projects/heroes-aya-pools/AG_Thongjuea/Result/bulkWGS/mitochondria/redeem/pool3/final/StrandBiaseBlackList'

Best
Iman