Results for "gz"
Bio-Scripts
Trim the reads in loop using Trimmomatic !
for infile in *_1.fastq.gz do base=$(basename ${infile} _1.fastq.gz) trimmomatic PE ${infile} ${base}_2.fastq.gz \ ${base}_1.trim.fastq.gz ${base}...m.fastq.gz \ ${base}_2.trim.fastq.gz ${base}_2un.trim.fastq.gz \...957 days ago
Command line to create blast uniref database !
...cbi.nlm.nih.gov/blast/executables/release/2.2.26/. wget ftp://ftp.uniprot.org/pub/databases/uniprot/uniref/uniref90/uniref90.fasta.gz gunzip -v uniref90.fasta.gz bin/pfilt uniref90.fasta > u...953 days ago
Command line to download blast database / protein
...p.ncbi.nlm.nih.gov/blast/db/ # Database detail / description nr.*tar.gz | Non-redundant protein seque...run this to download wget 'ftp://ftp.ncbi.nlm.nih.gov/blast/db/nr.*.tar.gz' #cat them into one cat n...946 days ago
Download desire version of Blast software !
...lm.nih.gov/blast/executables/blast+/2.6.0/ncbi-blast-2.6.0+-x64-linux.tar.gz #unpacking blast tar -zxvf ncbi-blast-2.6.0+-x64-linux.tar.gz #Slurm template #!/bin/...945 days ago
- ...4v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t addslash=t...4v1_genomic.fna_upper.diploid.fasta.gz \ illuminanames=t addslash=t...6/reformat.sh \ in=illumina1.fastq.gz in2=illumina2.fastq.gz out=il...maxlength=30000 \ out=pacbio.fastq.gz > random_reads_pacbio.log 2>&...
931 days ago
Bash script to simulate a genome !
...se bases, also compress with bgzip # https://github.com/lh3/s...174v1_genomic.fna_upper.fasta.gz \ ow=t \ vcf=GCA_003401745....rom the "diploid" reference bgzip -@75 -dc GCA_003401745.1_AS...nomic.fna_upper.diploid.fasta.gz \ illuminanames=t addslash=t...920 days ago
Extract fasta header with ids !
#Extract all the fasta header name with certain ids kraken --db ../../../../DATABASE/minikraken_20171019_8GB.tgz out.fa more out.fa_class.txt | grep "227859" | awk '{print $2}'...879 days ago
Install Install Gffcompare on Ubuntu / Linux
...# download and extract cd ~/workspace/bin wget http://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.9.8.Linux_x86_64.tar.gz tar -xzvf gffcompare-0.9.8.Linux_x86_64.tar.gz # make symlink ln -s ~/wo...826 days ago
- ...ept the installation location. ## download and extract cd ~/workspace/bin wget https://cran.r-project.org/src/base/R-3/R-3.5.1.tar.gz tar -zxvf R-3.5.1.tar.gz ## configure the installat...
826 days ago
Install StringTie on ubuntu / Linux !
...# download and extract cd ~/workspace/bin wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.0.Linux_x86_64.tar.gz tar -xzvf stringtie-1.3.0.Linux_x86_64.tar.gz # make symlink ln -s ~/wo...826 days ago
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