Tried to run on single strand mode, not working

[ryanpe13002]

To whom it may concern,

Hi! My name is Ryan Englander, I am an MD/PhD student at the Jackson Laboratory for Genomic Medicine. I am trying to use this package to check the strandedness of some single end RNA-seq data.

I installed this package using "pip3 install how_are_we_stranded_here", but unfortunately, it keeps throwing an error that R2 is required when I run with the command:

check_strandedness --gtf "$GTF" --transcripts "$FASTA" -n 500000 --reads_1 "$FILENAME" -k "$INDEX"

How do I install the most recent version that supports single end data?

Thanks so much,
Ryan

[Nick-Nunley]

I am having the same exact issue and I am running v1.0.1

[Nick-Nunley]

I don't think they have released the changes yet.

I checked the script in my site-packages directory and it still has --reads_2 set to required = True (different from the latest commits on this repo).