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KindLab / scDamAndTools

A set of functions for the processing of raw data generated by scDam&T-seq.
MIT License
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Count Statistics file not generated #1

Open StarkTS98 opened 1 year ago

StarkTS98 commented 1 year ago

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.

krooijers commented 9 months 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