Results for "r"
Bio-Scripts
...s/setu/setu$ sudo apt install r-base-core [sudo] password for vik:...Get:43 http://in.archive.ubuntu.com/ubuntu bionic...untu bionic/universe amd64 r-cran-kernsmooth amd64 2.23-15-3b...fsg-2) ... Setting up libalgorithm-merge-perl (0.08-3) ......1118 days ago
Install trimmomatic using Conda !
...ads/setu/setu$ conda install -c bioconda trimmomatic Collecting package metadata (current_repodata.json): done Sol...er version of conda exists. pkgs/main::certifi-2021.5.30-py37h06a4308_0...############################### | 100% trimmomatic-0.39 | 144 KB...1118 days ago
Install grabseqs using conda !
vik@vik-Lenovo-ideapad-320-15ISK:~/Downloads/setu/setu$ conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1118 days ago
Bash script to check installed bioinformatics program !
allTools=(bwa mummer trimomatic) decFlag=0; for name in ${allTools[@]}; do #echo "enter your package name" # read name...echo " $name not installed :: Try installing $name with conda...echo "Install all the missing sotware first" exit fi...1110 days ago
- ...hit Collecting package metadata (current_repodata.json): done Solv...done ## Package Plan ## environment location: /home/anacond...-64::megahit-1.2.9-h2e03b76_1 Proceed ([y]/n)? y Download...##################### | 100% Preparing transaction: done Verifyi...
1110 days ago
- ...ollecting package metadata (current_repodata.json): done Solv...ta.json, will retry with next repodata source. Collecting pa...libxslt conda-forge::libxslt-1.1.33-h15afd5d_2...################### | 100% Preparing transaction: done Ver...
1110 days ago
- ...gi Collecting package metadata (current_repodata.json): done Solv...done ## Package Plan ## environment location: /home/anacond...in::jemalloc-5.2.1-h2531618_5 Proceed ([y]/n)? y Download...######################### | 100% Preparing transaction: done Ver...
1110 days ago
- ...sh Collecting package metadata (current_repodata.json): done Solv...done ## Package Plan ## environment location: /home/anacond...-64::seqwish-0.4.1-h2e03b76_1 Proceed ([y]/n)? y Download...############### | 100% Preparing transaction: done Verifying tra...
1110 days ago
Corona variant calling steps !
...name "*.fasta" | while IFS= read -r my_file do filename=...ta) echo $basename mkdir -p results/sam results/bam re...ned.sam samtools view -S -b results/sam/$basename.aligned.s...$basename.bcf vcfutils.pl varFilter results/bcf/$basename.v...1109 days ago
- #Long reads bedtools bamtofastq -i input.bam -fq output.fastq #For paired-end reads: samtools sort -n input.bam -o input_sorted.bam # sort reads by identifier-name (-n) bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq
1060 days ago
