Sara Oppenheim

agat_sp_load_function_from_protein_align.pl - works only for Exonerate via MAKER.

20

I used pblat to align proteins to my draft genome, then used psl2gff to generate a gff3 file. When I run agat_sp_load_function_from_protein_align.pl like so: agat_sp_load_function_from_protein_align.pl --annotation manage_functional_annotation/strict_filter_A_atri_tm2_pnm_braker_plus_EDTA.gff3 -pgff pblat/Combined_insect_proteins2A_atri_genome_m2.gff -pfasta...

I installed blobtools with conda. Everything worked fine up until blobtools plot, at which stage I got no output and no error. Instead regardless of the command formation I just...

Hello. I'm finding that plotHeatmap is more useful for heatmaps than the "heatmap" option in plotProfile. But plotHeatmap has one big problem: it prints ALL the heatmaps in one row!...

I have sample groups that I'd like to cluster. If my samples are 1-10 and every 2 are the same species/tissue/whatever, can I do something like --clusterUsingSamples (1 2) (3...

I am struggling to get computeMatrix to complete. It worked fine with a set of bed files for individual chromosome regions, with 95 single region beds that look like this:...

hierarchy of evidence?

1

I am using braker on some hymenopteran genomes. I have RNA-Seq data and have generated a set of training proteins from OrthoDB. When I run busco on my genome, I...

Retrain using braker.gtf + new proteins

1

After completing Braker+TSEBRA, I find that there are Busco genes called on the genome that are not present in the set of predicted amino acids. These Busco genes mostly are...

Add a resume mechanism

3

I work on a scheduled cluster. Sometimes my jobs time out. Rather than start fresh, I would like sortmerna to resume at the point where it was shut down.

I have been struggling with exonerate to GFF3 for use with IGV, no solution I found or created was really what I needed. Today I discovered your process_exonerate_gff3.pl and it...

For my diploid organism I have the "hap1" and "hap2" assemblies from hifiasm. Could I use these as parents in order to apply HiC scaffolding to the hap assemblies rather...