config file

[aheravi]

Hi, Nice work! Congrats!

Two questions:

1- Can I use the config file from the example ("SIRV_config.json") to run my human datasets?

2- Also, I could not activate the environment after installing your software, the error below, and I guess I still can run it without activating the env. Is that correct? I am not getting any error if I run your software without activating the env.

I tried to export the env path and also ran "conda.sh" before running the command with no luck. Here is what I get if I try to activate the env:

conda activate FLAMES

CommandNotFoundError: Your shell has not been properly configured to use 'conda activate'.
To initialize your shell, run

    $ conda init <SHELL_NAME>

Currently supported shells are:
  - bash
  - fish
  - tcsh
  - xonsh
  - zsh
  - powershell

See 'conda init --help' for more information and options.

IMPORTANT: You may need to close and restart your shell after running 'conda init'.

[LuyiTian]

for 1). I would recomment you try config_sclr_nanopore_default.json and change "strand_specific":-1, depending on your protocol. Normally if it is a bulk cDNA nanopore sequencing data then it wont be strand specific, and you should change the paramater from -1 to 0.

for 2). I am not sure what the error is. maybe try conda init first. hope this would help: https://stackoverflow.com/questions/55507519/python-activate-conda-env-through-shell-script

[aheravi]

Hello, With regard to the strand specificity value in the config file, is it just two values either -1 for strand-specific or 0 for un-stranded or different numbers based on the strand-specific protocols? The protocol we used here is "fr-secondstrand", in other words, it is "First read transcription strand" (10X-chemistry is "Single Cell 3' v3").

[LuyiTian]

The nanopore sequencing protocol is not strand specific but the 10X single cell protocol is. if you use match_cell_barcode for barcode detection and trimming then the output should be in the reverse complement and you can set "strand_specific":-1. Otherwise if you are still not sure you can use "strand_specific":0, it does not make a big difference anyway.