run_rnaseqc.py unrecognized arguments: --unpaired

[yingsun-ucsd]

I am currently using the GTEx RNA-seq pipeline for my datasets, and it has been performing very well. However, I have encountered some samples that are single-stranded. It appears that run-rnaseqc.py is not functioning correctly for these samples, possibly because it defaults to paired-end reads. To address this, I intend to use the -u, --unpaired option to allow quantification of unpaired reads, which is necessary for single-end libraries. However, it seems that the Docker container does not accept this argument. I reviewed the documentation but could not find a solution. Does anyone have experience with this issue and can provide guidance on how to properly use this option with Docker? Thanks a lot!

nohup: ignoring input
HPAP-022_alpha
usage: run_rnaseqc.py
       [-h]
       [-o OUTPUT_DIR]
       [--stranded {rf,fr}]
       [--bed BED]
       genes_gtf
       bam_file
       prefix
run_rnaseqc.py: error: unrecognized arguments: --unpaired