Results for "IT"
Bio-Scripts
Find and replace in multifasta or fasta header with perl onliner
You have a fasta file and you want to replace: "|" You are told to replace that by "_" perl -i -p -e "s/\|/_/g" genome.fasta -i = inplace editing -p = loop over lines and print each line (after processing) -e = command line script1676 days ago
- ...cf file # $2 = input bam file # $3 = output QV file module load samtools NUM_BP=`samtools depth $2 | perl -e '$c = 0; while(){chomp; @s = split(/\t/); if(scalar(@s) >= 3){$c...
1665 days ago
Samtools commands for bioinformatician !
...samtool view -c -f 4 sal_sej.bam ### count reads by quality value specified (-q) (>=) # -q : minimal quality value samtools view -q 42 -...current version and commands ### calling snp and indels with no frequency threshold # om...1664 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pull the sequence data (...chive. fastq-dump is in the SRA toolkit. It allows directly downloadi...sequencing run ID fastq-dump --split-files SRR1770413 #SRA stor...STQ for further processing. The --split-files part of the command ens...1620 days ago
Bash script to alignment of short reads against reference genome !
....sorted.bam SRR1770413.bam ##Breaking it down by line: #alignment with bwa: bwa mem -t $threads -R...RR1770413.raw.bam --- sort the BAM file, writing it to .sorted.bam. #marki...jor change from bwa mem is that we'll tell it we're working with short read...1620 days ago
Install Samtools, Bcftools and htslib on Ubuntu !
...sesw5-dev sudo apt-get install liblzma-dev cd /usr/bin wget https://github.com/samtools/htslib/releas...tar -vxjf htslib-1.9.tar.bz2 cd htslib-1.9 make cd .. wget https://github.com/samtools/samtools/rele...1619 days ago
Bash commandline to install Anaconda !
#The line begins with $ are the commands $ mkd...8ec71_1 ... installing: graphite2-1.3.13-h23475e2_0 ... inst...b8bf9_0 ... installing: libedit-3.1.20181209-hc058e9b_0 ......0.2.0-py37_0 ... installing: itsdangerous-1.1.0-py37_0 ... i...... installing: prompt_toolkit-2.0.9-py37_0 ... installing:...1616 days ago
Bash command to install Miniconda !
.... connected. HTTP request sent, awaiting response... 200 OK Length...- idna==2.8=py37_0 - libedit==3.1.20181209=hc058e9b_0...- six==1.12.0=py37_0 - sqlite==3.30.0=h7b6447c_0 - tk...ed. Do you wish the installer to initialize Miniconda3 by running...1616 days ago
Bash command to install bwa, samtools, picard !
...pkgs/main/linux-64::libcurl-7.67.0-h20c2e04_0 libdeflate bioconda/linux-64::libdeflate-1.2-h516909a_1 libedit pkgs/main/linux-64::libedit-3.1.20181209-hc058e9b_0 li...1616 days ago
Bash command to install GATK, Bedtools and SnpEff !
...36h6115d3f_0 74 KB r-bitops-1.0_6 | r36...96ca727_0 164 KB r-magrittr-1.5 | r36h61...727_0 159 KB r-viridislite-0.3.0 | r36h6115d3...f8-1.1.4-r36h96ca727_0 r-viridislite pkgs/r/noarch::r-viridi...1616 days ago
