Lev Litichevskiy

Annotation of metagenomic reads is very slow

2

Hello, I am trying to use EggNOG to annotate gene function for metagenomic reads. I am following the [instructions](https://github.com/eggnogdb/eggnog-mapper/wiki/eggNOG-mapper-v2.1.5-to-v2.1.8#Setting_up_large_annotation_jobs) for doing the homology search separately from the annotation step. The...

Confusion about filter_taxa and filter_obs

3

Hello, Thank you for developing MetaCoder. I am enjoying the package so far. I am trying to filter my dataset before plotting heat trees, but instead of throwing counts away...

Why remove trimmed reads?

3

Hello, I'm wondering if you could please explain why the default is to remove reads with adapters. My intuition is that it would be fine to keep reads that are...

Related to our chat, @rajivnarayan, the methods that we’ll need for the tutorial are ds_get_meta, transpose_gct, ds_corr, and merge_two.

"Bus error" -- issue with snakemake or conda?

1

Hi Charlie, Sorry that you're hearing from me so soon. Hit another snag. I think this is related to which conda environment snakemake is trying to use? Not a reprex,...