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cmdoret / Acastellanii_genome_annotation

Reproducible container-based pipeline for the annotation of the Acanthamoeba castellanii genome
GNU General Public License v3.0
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custom RNAseq data #2

Closed lalalagartija closed 1 year ago

lalalagartija commented 1 year ago

Hi, Is it possible to run your pipeline with funannotate installed with docker rather than conda ? Second question : is it possible to add custom rnaseq data in addition to yours ?

Thank you very much,

cmdoret commented 1 year ago

Hi @lalalagartija

It should be possible to use docker, either by specifying individual images using Snakemake's container directive or using the new --containerize feature (I've never tried it.) So in brief, yes but some changes are needed. I just added a license, so you're welcome to fork or even make a PR if you feel like it.

It should be possible to use custom RNAseq data by changing the SRA identifiers in the units.tsv file. I've not tried it, so there may be unexpected behaviours.

lalalagartija commented 1 year ago

Great thanks, I will let you know if I manage.

another question : are your annotations of your assembly GCA_021020605.1 available somewhere without having to run the pipeline ?

cmdoret commented 1 year ago

You can find the assembly and corresponding annotations used in the paper in the associated Zenodo record.

I seem to remember the assembly on NCBI is an improved version that was submitted by our canadian colleagues. I will put you in touch.