I've been trying to run scTE on the provided test BAM file, however using the parameters -CB CR -UMI UR gives the error message that the bam file has no cell barcodes information and that I should set CB and UMI to False. Prior to running scTE, I've loaded the virtual environment from conda to ensure I have all the required packages installed.
The command that I'm entering is
$ scTE -i test.bam -o test -x mm10.exclusive.idx --hdf5 False -CB CR -UMI UR
With the error message being ERROR : The input file /scratch/st-mtokuy01-1/awang00/scTE/Data/test.bam has no cell barcodes information, plese make sure the aligner have add the cell barcode key, or set CB to False
Any advice on what I'm doing wrong would be appreciated. Thanks
EDIT: I was missing samtools, so once I got that loaded in, then it was able to recognize the CR:Z and UR:Z tags. However, just like #48, I'm receiving the message INFO : Detect 0 cells expressed at least 200 genes, results output to test.csv.
Hi there,
I've been trying to run scTE on the provided test BAM file, however using the parameters -CB CR -UMI UR gives the error message that the bam file has no cell barcodes information and that I should set CB and UMI to False. Prior to running scTE, I've loaded the virtual environment from conda to ensure I have all the required packages installed.
The command that I'm entering is
$ scTE -i test.bam -o test -x mm10.exclusive.idx --hdf5 False -CB CR -UMI URWith the error message being
ERROR : The input file /scratch/st-mtokuy01-1/awang00/scTE/Data/test.bam has no cell barcodes information, plese make sure the aligner have add the cell barcode key, or set CB to FalseAny advice on what I'm doing wrong would be appreciated. Thanks
EDIT: I was missing samtools, so once I got that loaded in, then it was able to recognize the CR:Z and UR:Z tags. However, just like #48, I'm receiving the message
INFO : Detect 0 cells expressed at least 200 genes, results output to test.csv.