NicMAlexandre
NicMAlexandre
We tried running hifiasm with and without the -I0 argument as we know that relative to other vertebrates, the species of interest has a highly homozygous genome. Because we were...
1. I have OmniC data instead of HiC, I assume I can run the following code? hifiasm -o HG002.asm --h1 read1.fq.gz --h2 read2.fq.gz HG002-HiFi.fq.gz 2. Do I run Hifiasm without...
The faidx for my largest chromosome in the original assembly is as follows: Chr1 196345723 6 60 61 The faidx for rawMask_35.fa and mask_35_50.fa show the following: Chr1 5609878 6...
Hello, After generating a library of repeats based on repeatmodeller and other software like LTRharvest and LTRRETREIVER, I ran the following using the RepeatMasker software. The assembly I provided does...
Hello, We were discussing potential sources of error and I wanted to ask the developers what their thoughts on this would be. Suppose the mean insert size is 149 base...
Hello, I am using funannotate 1.8.13 and am trying to integrate my interproscan results with my gff file. funannotate annotate --gff ../GFFfiles/S1_mod.gff --fasta ../Genomefiles/S1.fasta \ -s "S1" --iprscan S1.xml --eggnog...
Hello, Let's say I want to call a consensus with two conditions: 1. Don't assume reference when variant is missing, print N. 2. At heterozygous sites, print the longer allele,...
Hello, **I am getting the following error:** [racon::Window::generate_consensus] warning: contig 56 might be chimeric in window 312! /var/slurmd/job3892879/slurm_script: line 9: 38316 Bus error **Full Error Message:** [racon::Polisher::initialize] loaded target sequences...
Hello, 1. I have a chromosome (Chr1) that is 196345723 bp in length. 2. psmc/utils/./splitfa Sept22Assembly.fasta 35 | split -l 20000000 #This step produced three files and I confirmed the...
Hello, I I am running the pre-ma.bf script like so: hyphy hyphy-analyses/codon-msa/pre-msa.bf --input combined_seq.fasta I am running on a large memory node (1.5 Tb Memory) and get the following error:...