Open StarkTS98 opened 1 year ago
Indeed, this is reproducible, but only when --outfile
is not given.
Without --outfile
a table is printed to STDOUT.
See: https://github.com/KindLab/scDamAndTools/blob/3c907402338295f6e6809c82ac804b755a167746/scripts/generate_celseq_counts.py#L228
Hello, I am new to the scDamAndTools. I am following the tutorial given on the repository. So, I am using the
generate_celseq_counts.py
for generating UMI-unique transcript counts. I have my reference genome index files, GTF file and the aligned .bam files which creates a count file correctly. I also want to save the count statistics and the--save-stats
argument allows one to do that. However, after running the script, it does not generate a stats tsv file for me. I have checked, my version of scDamAndTools does support the--save-stats
argument. I tried giving a file name for saving the stats but it doesn't allow that. Any help would be appreciated.