1779 days ago
Samtools commands for bioinformatician !
## count mapped reads samtools view -c -F 260 mapping_file.bam ### converting sam file into fasta samtools fasta reads_mapped.sam > reads.fasta ### c...reads # and rows: total reads, duplicates, mapped. samtools flagstat sorted...1659 days ago
Perl script to remove duplicated lines !
...-- next line: $next_line$/"; print $_ if $_ ne $next_line; } continue { $_ = $next_line; } print $_ if eof; } __DATA__ apple apple plum vinegar apple ban...1616 days ago
Bash script to alignment of short reads against reference genome !
...ed.bam. #marking PCR duplicates: sambamba markdup SRR1770413.raw.sorted.bam SRR1770413.bam --- this marks reads which appear to be redundant PCR duplicates based on their read mapping position. It uses the sam...1615 days ago
1615 days ago
Install Samtools, Bcftools and htslib on Ubuntu !
#Inspired from online search sudo apt-get update sudo apt-get install gcc sudo apt-get install make sudo apt-get install libbz2-dev sudo apt-get install zlib1g-dev sudo apt-get install libncurses5-dev sudo apt-get install libncursesw5-dev...1614 days ago
Bash commandline to install Anaconda !
...6.1.2-h6c8ec71_1 ... installing: graphite2-1.3.13-h23475e2_0 ... i....38.0-h7b6447c_0 ... installing: snappy-1.1.7-hbae5bb6_3 ... insta...5-py37h7b6447c_0 ... installing: heapdict-1.0.0-py37_2 ... install...2.2-py37_1 ... installing: cryptography-2.6.1-py37h1ba5d50_0 ... i...1611 days ago
Bash command to install Miniconda !
...ting response... 200 OK Length: 71785000 (68M) [application/x-sh] Saving to: `M...47c_0 - conda==4.7.12=py37_0 - cryptography==2.8=py37h1ba5d50_0 -...package-handling-1.6.0-py37h7b6447c_0 cryptography pkgs/main/linux-64::c...1611 days ago
Bash command to install bwa, samtools, picard !
...4 pkgs/main/linux-64::gfortran_linux-64-7.3.0-h553295d_15 glib pkgs/main/linux-64::glib-2.63.1-h5a9c865_0 graphite2 pkgs/main/linux-64::graphite2-1.3.13-h23475e2_0 gsl...1611 days ago
Bash command to install GATK, Bedtools and SnpEff !
...| r36h29659fb_0 3.3 MB r-reshape-0.8.8 | r36h6115d3f_0 174 KB r-reshape2-1.4.3 | r36h29.../r/linux-64::r-rcpp-1.0.1-r36h29659fb_0 r-reshape pkgs/r/linux-64::r-...1611 days ago