Issues with longQC

Question

[SethJ]

Sorry if I'm missing something blindingly obvious here.

I've got some long read RNA-seq data (PacBio converted into fastq.gz). I want to run a QC tool on the data. I've run fastp and fastqc which gave very different results. I've read in a couple of places that fastqc in particular isn't great for long read RNA-seq data. I wanted to run longqc. I can't use the docker container because of the way the cluster I'm on is setup. I downloaded it via conda, when I try to run any command it doesn't recognise it existing. Even just trying to run longqc without any parameters doesn't work. How am I meant to run it? Is there an obvious way I'm not familiar with. If not, can anyone recommend some tools that are recommended for doing initial QC of long-read RNA data?

(long_read) [profile]$ longqc
-bash: longqc: command not found
(long_read) [profile]$ python longqc.py
python: can't open file 'longqc.py': [Errno 2] No such file or directory 

[GenoMax]

Have you followed the entire set of directions for the manual install, including installing minimap2?

[SethJ]

Short answer, yes. Longer answer: I already had minimap2 installed. When it didn't work at first I installed minimap2-coverage via conda, and when that didn't work I installed it as they suggested. I'd have thought that dependancies would throw issues later on though, not cause issues with knowing the function existed in the first place.

[GenoMax]

Page you linked stated that

Modified version of minimap2 named minimap2-coverage is also required.

As long as you have that installed and that is the only minimap2 in $PATH it should be ok.

This could simply be a case of configuring the right $PATH. Have you added the directory where you installed the software to your $PATH? Can you provide the full path to longqc.py? Make sure your python is v.3.7 or 3.9.