omarkr8

Is dada2 suitable for Nextera XT + viral genome ?

1

Hi, I have been wrangling some metabarcoding MiSeq data using dada2 and otu clustering to help simplify the search for recombinant sequences. I have managed to run through my make-shift...

Clarification on NGSpID output

3

I'm looking at the output from the pipeline and referring to text on the main page : "The final cluster information is given in a tsv file final_clusters.tsv present in...

flexible clustering ?

1

Is there a way to adjust clustering parameters? for example, some OTU pipelines will generate different number of bins depending on whether you want 98% or 95% similarity clusters. I...

hangs at start of simulation

5

Hi, I'm finding myself stuck at the start of simulations. Im running the metagenome sim. for example it will say : 2022-12-28 23:26:25: Read in seq1 2022-12-28 23:26:25: Read in...

Hi, very cool package, im trying to tidy the figures and wanted to know if the msabar + consensus can be adjusted visually. for example, perhaps shrunk height-wise to it...

run wont start. output is in same directory as data

12

I'm trying to start a run. filling the details in the webpage returns me to the top with an error about the output being the same directory as data (i'll...

Add option for min_depth

1

Just a suggestion, but would be nice to be able to still generate consensus with regions

Gupplyplex. illegal instruction, core dump

18

Finding strange output at the first step of the pipeline, im assuming it is trying to use guppyplex to collect demux data. output looks like ***RUNNING GUPPYPLEX COMMAND*** Illegal instruction...

I've yet to try the script myself, but curious how i could use it with output from a remote blast. it looks like the input fasta and database files are...