Results for "1"
Bio-Scripts
Perl script to run in parellel !
...::ForkManager->new( $n_processes ); for my $i ( 1 .. $n_processes ) { $pm-...UGUSTUS_CONFIG_PATH=/home/urbe/Tools/Alienomics_v1.1/augustus.2.5.5/config");...gc//; my $GCcontent = ($GCcount / $len) * 100; $sequence_data{$acc...1710 days ago
- # $1 = vcf file # $2 = input bam file # $3 = ou...;'` echo "num bp: "$NUM_BP NUM_SNP=`cat $1 |grep -v "#" | awk -F "\t" '{if (!match($NF, "0/1")) print $1"\t"$2"\t"$3"\t"$4...e 'chomp(@ARGV); $ns = $ARGV[0]; $nb = $ARGV[1]; print (-10 * log($ns/$nb)/l...
1628 days ago
Samtools commands for bioinformatician !
...++;s+=$3}END{print s/c}' ### one liner to count coverage breadth samtools depth -a sorted_dupremoved.bam | awk '{c++; if($3>0) total+=1}END{print (total/c)*100}' ### flagstat # output...1627 days ago
Bash script to download SRA file !
...data from a particular sequencing run ID fastq-dump --split-files SRR1770413 #SRA stores data in a par...ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra instant/reads/ByRun/sra/SRR/SRR177/SRR1770413/SRR1770413.sra...1583 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_1.fastq.gz SRR1770413_2.f...\ | samtools view -b - >SRR1770413.raw.bam sambamba sort...wa mem -t $threads -R '@RG\tID:K12\tSM:K12' --- this says "alig...the BAM file: sambamba sort SRR1770413.raw.bam --- sort the BA...1583 days ago
Install Samtools, Bcftools and htslib on Ubuntu !
...get install libbz2-dev sudo apt-get install zlib1g-dev sudo apt-get install li...s://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 tar -vx...oad/1.9/samtools-1.9.tar.bz2 tar -vxjf samtools-1.9.tar.bz2 cd samtools-1.9 m...1582 days ago
Bash commandline to install Anaconda !
...installing: python-3.7.3-h0371630_0 ... Python 3.7.3 insta...d415_1 ... installing: lz4-c-1.8.1.2-h14c3975_0 ... install..._2 ... installing: dask-core-1.1.4-py37_1 ... installing: d...nstalling: pyqt-5.9.2-py37h05f1152_2 ... installing: pyrsist...1579 days ago
Bash command to install Miniconda !
...t-Linux-x86_64.sh --2020-02-01 13:25:25-- https://repo.anacon...a3-latest-Linux-x86_64.sh' 100%[==========================...==4.36.1=py_0 - urllib3==1.24.2=py37_0 - wheel==0.3...onda3/shell/condabin/Conda.psm1 no change /data/sata_dat...1579 days ago
Bash command to install bwa, samtools, picard !
...efaults/linux-64::numba==0.43.1=py37h962f231_0 - defaults/linux-64::ana...Total: 21.8 MB The following NEW pac...pkgs/main/linux-64::xz-5.2.4-h14c3975_4 Proceed ([y]/n)?...pkgs/main/linux-64::pango-1.42.4-h049681c_0 pcre...1579 days ago
Bash command to install GATK, Bedtools and SnpEff !
...-------------- certifi-2019.11.28 | py38_...| r36ha65eedd_4 102 KB r-labeling-0.3...1.9 MB wheel-0.34.1 | py3...########################### | 100% r-glue-1.3.1 | 1...1579 days ago
