-
@malloryfreeberg Hi Mallory,
It's not clear from https://github.com/galaxyproject/training-material/blame/50518e9db648d8ac77ea7ab34f9caf595a78621b/topics/transcriptomics/tutorials/srna/tutorial.md#…
-
## Is your feature request related to a problem? Please describe
We don't have test data available in the https://github.com/nf-core/test-datasets repository for most of the modules https://github.…
-
## Expected Behavior
GFF with the found profiles.
## Current Behavior
Stopping at collectoptimalset step.
## Steps to Reproduce (for bugs)
easy-predict --num-iterations 2 --metaeuk-tcov 0.4 -…
-
My genome is small (180 Mb) and haploid. As BRAKER2 evidence I have good mapped RNA seq data from this organism, and ~550 same-species/close-species protein sequences.
Formerly I would use addi…
-
#### Are you using the latest version of [samtools](https://github.com/samtools/samtools/releases/latest) and [HTSlib](https://github.com/samtools/htslib/releases/latest)? If not, please specify.
sam…
-
Hello,
I was able to use mcorr for whole-genome alignments, but I was wondering if it's possible to use it for core genome alignments.
I tried extracting a core genome alignment from my whole-ge…
-
Hi,
I have a question of one to one block.
For example, use this script to align hg38 to mm10:
`
lastal -P8 -D1e9 -m100 -p my.train myDB genome2.fa |last-split -f=MAF+> many-to-one.maf
last…
-
Hello,
I do not know if this is intended pipeline behaviour, but when I lounch the following command:
`nextflow run main.nf --genomes "../test/Genomes/*.fasta" --annotations "..//test/GTF/*.gtf" --…
-
I am trying to run BRAKER2 with 8 CPUs on a moderately large and complex nematode genome (150 Mb) for which I have RNA-seq data (in an indexed and sorted BAM file). Try as I may, I can only get BRAKE…
-
I just ran TELR using the following command:
telr -i /path/to/long/reads/1034.fastq -r /path/to/refgenome/Mguttatus_256_v2.0.fa -l /path/to/consensuslib/allTE-families.cons --out TELR_annotations
…