Chris Keeling
Chris Keeling
Hello, I notice that I don't get similar results from ref=reference.fa fa=scaffolds.fa as I do with ref=scaffolds.fa fa=reference.fa. I am looking at one sequence in reference.fa, and 4 sequences in...
Hello all, I have a transcriptome assembly (with no reference genome available) that appears to have some gDNA contamination such that I am seeing very similar contigs with retained introns...
Hello, I have HiC (Chicago) and HiC data, and a gfa file for the draft assembly to scaffold. I am trying both ways, but conceptually, would there be any problem...
Hello, Reading your paper, it suggests that SALSA2 will iterate until the majority of the joins in an interaction are marked as incorrect, and then the penultimate iteration is used...
Hello, I'm using the following command with braker 2.1.6: ```bash braker.pl --genome genome.fa --UTR=on --stranded=+,- --bam=merged_fwd.bam,merged_rev.bam --softmasking --cores 48 ``` I get the following error: ``` ERROR in file /usr/local/bin/BRAKER/scripts/braker.pl...
Hello, I am running BRAKER within a Singularity container. I was having errors with Braker saying that java wasn't version 1.8 when in fact it was. It turned out that...
Hello @ryought It is not obvious from the .assembly output what if anything has changed by running hic-hiker. Could you please explain the format of the stdout, specifically those lines...
Can you suggest starting parameters for GC-MS data?
I get a warning every time I start RStudio before any code has been executed: ``` Registered S3 methods overwritten by 'treeio': method from MRCA.phylo tidytree MRCA.treedata tidytree Nnode.treedata tidytree...
Hello @natacha-beck I am using the Docker version with apptainer. I get the following error at step 13: ``` ... 12) Identify start codons; identify gene fusions... 13) Find extra...