error: unrecognized arguments: --n_cells auto

[defendant602]

Hi @andrewprzh

I tried isoQuant on my nanopore long-read single cell data, my commands were like:

isoquant.py --mode tenX_v3 \
  --barcode_whitelist  3M-3pgex-may-2023.txt.gz  --n_cells auto \
  --fastq reads.fastq.gz --reference genome.fa --genedb genes.gtf \
  --data_type nanopore -o output_dir

but an error was thrown:

usage: isoquant.py [-h] [--full_help] [--test] [--output OUTPUT] [--prefix PREFIX] [--labels LABELS [LABELS ...]] [--reference REFERENCE] [--genedb GENEDB]
                   [--complete_genedb] [--bam BAM [BAM ...] | --fastq FASTQ [FASTQ ...] | --unmapped_bam UNMAPPED_BAM [UNMAPPED_BAM ...] | --yaml YAML]
                   [--illumina_bam ILLUMINA_BAM [ILLUMINA_BAM ...]] [--read_group READ_GROUP [READ_GROUP ...]]
                   [--data_type {pacbio_ccs,pacbio,nanopore,ont,assembly,transcripts}] [--stranded STRANDED] [--polya_trimmed {none,all,stranded}] [--fl_data]
                   [--threads THREADS] [--resume | --force] [--check_canonical] [--sqanti_output] [--count_exons] [--version]
isoquant.py: error: unrecognized arguments: --n_cells auto

I tried both version 3.12.2 and version 4.0.0 but got the same error, when I removed "--n_cells auto" from my commands , everything went fine.

Is the "--n_cells" parameter still active ? Looking forward to your reply.

Bestwishes.

[andrewprzh]

Dear @defendant602

Apologies, this option is only available in the master branch and is set to be released in 4.1. The documentation is build from the master branch, probably I should change that to avoid confusions.

Best
Andrey