Aligning Metagenome-assembled genomes to metatranscriptomics libraries command line?

ablab / metaGT

Pipeline for metagenome and metatranscriptome joint assembly

MIT License

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Aligning Metagenome-assembled genomes to metatranscriptomics libraries command line? #5

Closed JSSaini closed 1 year ago

JSSaini commented 1 year ago

Hi, I would like to align the list of metagenome-assembled genomes to merged-metatranscriptomics libraries. Please suggest a reasonable command to run MetaGT? I tried the following, but it complains about genome input, maybe because of absolute paths.

nextflow run /media/bioinfoteam/SCRATCH_1TB/jssaini_scratch/github/metaGT/metaGT m -genome '*/media/bioinfoteam/SCRATCH_1TB/jssaini_scratch/Aline_MAGs/Aline_JS_combo/All_MAGs_work_13_Feb/stag_bins/drep_results_90_10/dereplicated_genomes/bakta_derep_mags_results/MAGs_2.5k/*.fa' --transcriptome '*.fastq'

Unknown option: -genome -- Check the available commands and options and syntax with 'help'

And how to open help documentation? Thank you for your kind assistance.

andrewprzh commented 1 year ago

Dear @JSSaini

Sorry for the late response.

To get available options you can run nextflow run metaGT -profile conda --help. I'll add information to the README soon.

To provide assembled metagenomes the option is correct except you forgot a second dash: --genome To provide RNA reads I suggest to use --rna_reads option.

If you encounter more problems do not hesitate to contact and send me the error message.

All the best Andrey