Installing ggplot2 and its dependencies on Ubuntu !
...trying URL 'https://cloud.r-project.org/src/contrib/ellipsis_0.3....trying URL 'https://cloud.r-project.org/src/contrib/stringi_1.4.5...trying URL 'https://cloud.r-project.org/src/contrib/labeling_0.3....trying URL 'https://cloud.r-project.org/src/contrib/ggplot2_3.2.1...1552 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencing data. PROJECT=PRJNA257197 # The number of datasets to subselect from the project. N=5 # Get the project ru...1544 days ago
1528 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-Pro-3335-MT:~/Downloads...& answer key is released... Evaluation of genome assembly software based on lo...adsBy BioStar 409 days ago Evaluationgenomea...1514 days ago
Commands to install conda in Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ mkdir jittmp jit@jit...ate to cryptogr aphy: openssl The OpenSSL Project is a collaborative effort to...a-navigator-1.9.7-py37_0 ... installing: anaconda-project-0.8.2-py37_0 ... installing:...1514 days ago
Install Ragout genome assembler
$ conda install -c bioconda ragout Collecting package metadata (repodata.json): done Solving environment: done ## Package Plan ## environment location: /home/...1466 days ago
1444 days ago
get GC across the entire CDS !
#look at GC across the entire CDS. gffread -x - -g | \ seqtk comp - | \ awk -v OFS="\t" '{ print $1, "0", $2, ($4 + $5) / $2 }'1395 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.gz1368 days ago
Bash script to get intergenic region from genome files !
#For the intergenic region, we will require the size of the chromosomes. wget http://xxx.chrom.sizes cat xxx.ch...s | sed 's/^chr//' | sed 's/Cp/Pt/' > tmp mv tmp xxx.chrom.sizes gunzip -c genome_...1368 days ago