Sadik

Updating previous braker.gtf with addUTR output for non-fungal eukaryotic genome

1

In the first round BRAKER run ``` braker.pl \ --species=species \ --genome=genome.fna \ --hints=prothint_augustus.gff \ --bam=RNASeq.sorted.bam \ --etpmode \ --softmasking \ --AUGUSTUS_ab_initio \ --cores 8 \ --workingdir $wd_etpmode \ --nocleanup...

ltrdigest_complete.fas_DfamAnnotation.out' does not exist

7

Hi LTRpred is crushing after step 4. Dfam is manually downlaoded and kept in the directory where ltrpred set to run and assigned with annotate = "Dfam", Dfam.db = "dfam"...

Read Subsampling tool error

3

Hello, Could you please help me out? I am getting the following error message after running Read Sampling Tool and tried with different options (-T lr, -Tlr 0.2, -T l,...

I noticed that there are mm, gn, and go tags in the SAM/BAM file converted into PAF using pfatools. However, I couldn't find the definitions of these tags in the...