1440 days ago
1402 days ago
Command to sort the bed file !
#Command to sort the bed file sort -V -k1,1 -k2,2 test.bed1389 days ago
Bash script to get exon fragments from genome files !
#Exons are already defined in the GTF file, so we simply need to print lines that are marked exonic. gunzip -c genome_file.gtf.gz | awk 'BEGIN{OFS="\t";} $3=="exon" {print $1,$4-1,$5}' | bedtools sort | bedtools merge -i - | gzip > my_exon.bed.gz1366 days ago
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $P...1337 days ago
1216 days ago
Set up WGD environment using conda !
#Wgd cannot be installed directly with bioconda at present, so it is slightly troublesome to install, beca...ter) wgd zsh: correct 'wgd' to 'gd' [nyae]? n Usage: wgd [OPTIONS] COMMAND [ARGS]... Welcome to the wgd comma...1204 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
#Need to download i-adhore-3.0.01.tar.gz from https://wdiceryfd4rjn74bjhhtz2k5di--bioin...warn_unused_result [-Wunused-result] system(command.append(outputPath).c_str());...warn_unused_result [-Wunused-result] system(comma...1204 days ago
Command to create conda environment !
# using pip pip install -r requirements.txt # using Conda conda create --name --file requirements.txt #Using yaml conda env create -f environment.yml #Listing env conda env list #Create env with python36 conda create -n myenv python=3.61200 days ago
1163 days ago