SheepwormJM

Hi, I have 6 species, and my species tree has 5 nodes (N0 to N4), and I have 5 output .tsv files from the Phylogenetic_Hierarchical_Orthogroups analysis. However, in the N0.tsv...

Tiny bug - gtf output header

2

Using the ```agat_convert_sp_gff2gtf.pl``` to convert a gff3 file to a gtf file I found that the output gtf file had a slightly confusing header: ``` ##gtf-version X # GFF-like GTF...

Which output file is best?

1

Hi, I am slightly confused over the output files and wanted to check which one is best. As I understand it, the tree is made and including an outgroup improves...

How to find out the site_url to access a local docker desktop container remotely?

1

Hi, I am very new to docker (installed it to use HiGlass a few weeks ago). My windows laptop is struggling to locally host HiGlass, my data and anything else...

Question: How does the SNP window work?

5

Hi, I've been plotting files and realised that the SNP windows are the same co-ordinates for all my pairwise comparisons. But that some have 'nan'. Does this mean that windows...

Hi, Thank you for this really useful tool. I am looking for information as to which of the output directories are not deprecated. I understand from the github readme page...

Extracting original sequences

3

Hello, Thank you for DADA2. I have my output table of ASV sequences and their abundance following chimera removal. However, what I would really like is a way to get...

Multiple fasta sequences, but of different lengths

3

Hi, I think I may have an idea of the right answer to my question, but hoping to check I'm not going to do something stupid. I'm wondering if I...

Pooled samples and mosaic option

12

Hi, Just following on from the 2017 question 'Detection on Pooled Samples #21 '. Would using the --mosaic option be useful for pooled sequencing data? Or would you recommend running...