Georges Kanaan

Parsing input error

10

Hi @ArtRand, The following command which I believe to have executed on identical files in the past (perhaps on 0.3.0) seem to produce the error below now: ``` modkit dmr...

Ignore multiple mods in adjust-mods

1

Just a convenience feature would be able to do `modkit adjust-mods --ignore a,m`.

dmr multi doesn't handle replicates

1

Hi @ArtRand, Running the following: ``` modkit dmr multi -s methylation_10/brevundimonas_r-contigs/barcode01.bed.gz top -s methylation_10/brevundimonas_r-contigs/barcode02.bed.gz middle -s methylation_10/brevundimonas_r-contigs/barcode03.bed.gz bottom -s methylation_10/brevundimonas_r-contigs/barcode05.bed.gz top -s methylation_10/brevundimonas_r-contigs/barcode06.bed.gz middle -s methylation_10/brevundimonas_r-contigs/barcode07.bed.gz bottom -s methylation_10/brevundimonas_r-contigs/barcode08.bed.gz top...

Multi-base entropy

3

Hi Arthur, I was wondering if multi-base entropy (i.e. `--base A --base C`) is something that made sense/was planned?

Understanding output

1

Hello, I ran the tool on a FASTA file representing a genome which contains many different contigs. I used `python Promotech-master/promotech.py -g -i results/ -o results/` to generate the final...

Unclear modkit pileup `--region`

2

Hi Art, To pileup many different contigs I thought of doing `modkit pileup --region contig_1,contig_2` since the documentation says `Commas are allowed`. But that seems to not be correct? I...

find-motifs --contig failed to parse any bedmethyl records

5

Hey @ArtRand I'm having some issue running `finds-motifs` after `merge bed`. I get: ``` _My script: Finding enriched motifs for contig contig_100009 in metagenome_assembly_ > loading references from "mags//metagenome_assembly.fna" >...

Quality of life suggestion for motif bed

2

Hi @ArtRand Just an unimpactful quality of life suggestion. It would be nice to have a `--contig` option on `motif bed` to restrict to the passed contig. Just a small...

Entropy on strand

5

Hey @ArtRand, I just wanted to write to ask for a feature request for `entropy` which would be to make it "strand aware" by allowing us to specify the strand...

Documentation ambiguity

1

The docs for `sample-probs` say `-p` takes space separated floats, but in fact it takes comma separated floats.