Setup and long_read_wrapper.sh query

[ICA-D]

Hi there,
Thanks for your work in making such a useful tool. Great to see people looking at tackling the locus-specific TE analysis problem (and Telescope was a great tool for me too).

I noted a couple of issues with the long_read_wrapper script that I thought might be helpful to point out. The first was that ${name} isn't defined anywhere before it's used in the script, which throws up an error. I added this line before pychopper to fix it: name=$(basename "$long_fq" .fastq.gz).
The second is that I think the pychopper command is incorrect; the input file $long_fq should come first, followed by the ${long_fq}_pychopper.fastq.gz? Without this change in order, the script was searching for something like filename.fastq.gz_pychopper.fastq.gz to run pychopper on.
Finally, following the installation guidelines threw up some dependency issues for me due to openssl version clashes. I can share the conda list for the environment that did work for me if that's helpful, with updated python etc. I used the below to set up an environment that worked.

conda create -n LocusMasterTE_modern python=3.8 -c bioconda -c conda-forge -c defaults
conda activate LocusMasterTE_modern
conda install -c bioconda -c conda-forge pychopper pysam minimap2 samtools subread r-base

Thanks!

[LEESojung1998]

Hi,

First, I’m glad to hear that LocusMasterTE has been useful to you!
Thank you for pointing out a few issues—I’ll update them based on your comments.

Best,

Sojung