DaRinker

Is DeepFRI no longer being updated or supported?

3

Am interested in using DeepFRI in a new pipeline I'm writing, but am concerned (based upon the number and age of unaddressed Issues here) that DeepFRI is no longer supported.

FUN gene ID numbering seems inconsistent

7

I'm seeing inconsistent behavior in the default gene numbering in my annotations. For example: ` $ grep FUN_ DTO15.proteins.fa | head >DTO15_FUN_000001-T1 locus=DTO15_FUN_000001 >DTO15_FUN_000002-T1 locus=DTO15_FUN_000002 >DTO15_FUN_000003-T1 locus=DTO15_FUN_000003 >DTO15_FUN_000004-T1 locus=DTO15_FUN_000004 >DTO15_FUN_000005-T1...

PASA failure when running as job on cluster (but will run okay interactively)

8

**Are you using the latest release?** yes. running docker as singularity **Describe the bug** Trying to annotate a large number of genomes on local cluster. Using Singularity image with supporting...

Suddeny cannot run bwa-mem2 on shared cluster ( "ERROR: prefix too long!")

6

Same installation, same scripts, same environment (on my end). Previously I could simply execute: `bwa-mem2 index mygenome.fasta ` Now I get "ERROR: prefix too long!" I can remedy by changing...

QUESTION: what would cause a specie's proteins to be over-represented in the query field of the output?

4

I have a fasta with proteins from 10 closely related species (average about 12000 proteins per spcies) While the proteins from each species are very evenly distributed in the subject...

Question on kaiju classification from PacBio data

3

Looking for insight/confirmation that Kaiju is operating as expected. My results thus far are suggesting that kaigu is misclassify reads that are very string BLAST hits to divergent taxa. Specifically,...

Meaning of "UniqueReads" in genes.out file?

2

I have been comparing HTSeq (htseq-count) counts to TPMcalcualtor UniqueReads counts. I find them generally to be in very good agreement. However, there are occasionally some cases where HTSeq and...

When scaffolding against a high quality reference, what do outputs of "hybrid" scaffolds most likely indicate?

4

I am scaffolding several ONT+illumina assemblies (flye) against a T2T reference genome of a sister species. Each of my assemblies represents a specific strain of my species of interest--so while...

Best practices question--is "overfiting" to the reference sequence a problem?

3

I have 20 de novo hybrid genome assemblies (ONT plus Illumina; flye plus pylon polishing) of different strains of the same species. For an initial genome reference, we also have...

Is there an option to generate a PAE matrix along with the structural prediction? I would like compare the PAEs generated by of Alphafold2 and ESMfold with with those assigned...