Alex Predeus

Remove clipped bases?

3

I was wondering if it's worth adding the option to not remove the whole read with soft/hardclipping, but rather just trim the clipped reads? There's one obscure and no longer...

Very diverse pangenome?

1

Hello, I wanted to look at protein presence-absence of a broader group of genomes (several different orders from alpha-proteobacteria). Would you say it's possible with panX, or should I just...

Reproducing the analysis from Nature Biotech paper

7

Hi, Thank you for a really great tool and an exciting dataset! I'm trying to reproduce the analysis done in the Nature Biotech paper (https://www.nature.com/articles/s41587-022-01250-0). I've downloaded the processed data...

Hello, not sure if I'm doing something wrong, but the newest (linux) version of poretools does not seem to find fast5 files in a directory. I've made a test directory...

Selective k-mer generation?

3

Dear KrakenUniq team, I have a theoretical question - I was wondering if you could suggest something here. I am using KrakenUniq to classify bacterial reads from RNA-seq experiments. The...

Which Pavian version works with KrakenUniq reports?

2

Hi all, I remember using Pavian to load KrakenUniq reports, but it's been a while and I had to re-install both R and Pavian. Newest version (R4.4, Pavian 1.2.1) does...