pailloufat-stack

Hello, I have a Pacbio CCS assembly (I used hifiasm as assembler). I also have a reference genome assembly (~2.8Gb) which contains several 500pb gaps. I used `ragtag patch` to...

The purging step (-l 3) combined with the purge_dups tool

18

Hello, Is it suitable to run the `purge_dups` pipeline on my assembly obtained with the 0.15.1 version ? I assembled a low heterozygous genome (~1.1/1.2Gb expected size) , which gives...

Demultiplexing step between "lima" Pacbio tool and "removePrimers()" function

2

Hi Ben I have a pool of 24 samples (16S Pacbio) CCS reads. I wonder why I have such a difference of reads after the demultiplexing step between `lima` from...

Hello, Thanks for your very useful tool. I use the `kpPlotDensity` function to get a coverage graph. I would like to set up the y-axis values from the lowest coverage...

Hi, I ran DADA2 on my 3 datasets, then I got 3 "ps" phyloseq objetcs. I have the absolute abundaces for these 3 datasets. The thing I need is to...

Switch from a phyloseq object to a dada2 object

1

Hi, I have my `seqtab.nochim` and `tax `objects from the DADA2 pipeline. Then, I need to run a phylogenic tree on this seqtab matrix with `raxml` or `phangorn` but it...

Wrong Short Tandem Repeat size in vcf file

4

Hi, I work on 16 mice samples. I look at STR variants in 13 / 16 of them, which are heterozygous ; the 3 others are wild homozygous. What I'm...