Andrea Spitaleri

demultiplexing fast5

19

Hi From #14 It seems that MotifSeq could demultiplex a bundle of fast5 to retrieve the fast5 for each strains. Is this right? Or there is some options in Squiggle...

QIIME2_TREE fails running '-profile test,singularity' [not reproducible yet, please report when encountering!]

3

### Description of the bug I have download the ampliseq pipeline singularity as follow: nf-core download then I run nextflow run nf-core/ampliseq -profile test,singularity --outdir test but it fails with:...

pi cluster within-pool

11

Hi Chase - I have performed the within-pool using the vcf report as input. Now I have several output and I am trying to understand (after reading your papers and...

analysing within-host diversity

12

Hi I have read your exhaustive introduction and paper and I think it can be useful for my purpose. My interest is to study Ecoli within-host diversity for each sample....

index 50 is out of bounds

3

Hi I am trying to use convert_dataset.py on my simulation. I converted the xtc to pdb containing only CA, having 100,001 MODEL. The number of residues are 489 and I...

Hi I was trying to use this approach: https://github.com/Psy-Fer/CoVarPlot to plot the coverage as function of the pool in the artic V3 (see the example at the bottom of the...

duplicate in bam

2

Hi, I am using the pipeline to analyze my artic v3 SARS-CoV-3 data. I noticed that in aligned dir the bam file contains many duplicate and therefore could effect the...

Amend

1

Hi all, the TBAmend step require a lot of time in case of several inputs. I am wondering whether there an option in TBAmend by which adding new samples in...

Cant find chain

3

Hi there, thanks for the script! I am using to generate pdb with missense mutations. It works except for this: `pymissense O95477 abaca1 --maxacid 2224 --pdbpath 7tc0.pdb --tsv /tmp/alpha.tsv` Cant...