michoug

import table file

2

Hi, I have big tables that I want to include in my manuscript, but I would prefer it if they could be imported directly from an outside file as are...

placeholder legend

1

Hi I sometimes need to cite in my text a table that would not fit in the manuscript (such as a big excel file for example). Is it possible to...

Video tutorial for the interactive display

3

Hi, Sorry if it already exists, but I found the interactive display options a bit unclear. I would suggest to add a tutorial page on the different options to increase...

InvalidIndexError: Reindexing only valid with uniquely valued Index objects

10

Hi, I got this error from DRAM-v.py Here the command used `DRAM-v.py annotate -i ENSEMBLE_vRhyme/for-dramv/final-viral-combined-for-dramv_mod.fa -v ENSEMBLE_vRhyme/for-dramv/viral-affi-contigs-for-dramv_mod.tab -o annotation --threads 28 --verbose` Here the log ``` 5:04:00.646081: Getting hits from...

Excepted size prefilter and --disk-space-limit

3

Hi, I'm trying to run an annotation with a metagenome filtered with Eukrep of ~1115 MBp with your database based on Uclust. `easy-predict --threads 35 --slice-search -e 100 --metaeuk-eval 0.0001...

Works with metagenome ?

8

Hi, I got a metagenome assembly (filtered by Eukrep (https://github.com/patrickwest/EukRep)) and was wondering if BRAKER would be adapted for its annotation? If yes, which parameters would you choose? Best Greg

Support for QMaker and nQMaker from IQ-TREE?

1

Hi, Very nice software. I was wondering if you plan (or are already) supporting the new amino acid substitution models QMaker and nQMaker from IQ-TREE software? http://www.iqtree.org/doc/Estimating-amino-acid-substitution-models Thanks

Hi the command on line 30 doesn't take into account the $BINDIR variable to look for the database ``` my $bin = "$FindBin::RealBin"; $DBDIR ||= "$FindBin::RealBin/../db"; my $rna_hmmdir = "$bin/../db/hmm/rna";...

Suggestion : Run checkm on more than 1 MAG at a time

1

Hi, I have a few hundred MAGs that I want to taxonomically check and I realized that the checkm software is run MAG per MAG as are all the other...

Plotting Genera instead of OTUs

1

Hi, I was wondering if there was an "easy" way to plot genera (probably obtained by summing the OTUs that are in this genus) instead of OTUs? Best Greg