Results for "Command Line"
Top-level pages
To do sam to bam conversion, follow the following commands :- Code: $ samtools...amtools followed by the name of one of the samtools commands, you will get a few lines of help giving the correct syntax for that command,2305 days ago
Linux Commands Cheat Sheet for Bioinformatics and Computational Biology Professionals
...ing experience in writing one-liners. File System ls &mdash...p;— output the first 10 lines of file tail file —...— edit file alias name 'command' — create an alias for a command System shutdown &md...2294 days ago
Awk for Bioinformatician and computational biologist
...files to see if they contain lines that match with the specified p...ms the given actions for each line of the input.If the action is...e first field to $0 for third line (NR==3), we can use: $ awk '...for (INDEX in VARIABLE_NAME) command: $ awk '{i[$1]=1}END{for...2293 days ago
Some useful Bioinformatics links
...ssembly and Illumina polishing pipeline https://github.com/nanoporetech...corrected Long read Itegration Pipeline https://github.com/Generade-...://broadinstitute.github.io/picard/command-line-overview.html Chromos...jts/nanocorrect: Experimental pipeline for correcting nanopore reads...2255 days ago
Installing Bio::SCF perl module
...s http://bioinformaticsonline.com/blog/view/710/how-to-install...l-modules-manually-using-cpan-command-and-other-quick-ways install...ze of long... 8checking for inline... inlinechecking for mode_t......so"/usr/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- SC...2232 days ago
- To remove all line ends (\n) from a Unix text file: se.../g' filename.txt > newfilename_oneline.txt To get average for a col...ile: cat file_list.txt | while read line; do cp "$line" complete_datas...To keep only one copy of duplicated lines: awk '!seen[$0]++' To sum...
2231 days ago
Creating conda environment for python2.7
...on TIP: You can add much more to the conda create command. For details, run conda&...sl: 1.0.2o-h20670df_0 pip: 10.0.1-py27_0 python: 2.7.15-h1571d57_0 readline: 7.0-ha6073c6_4 setuptools:...2203 days ago
Frequent Paired-end reads (PE 2x100) mapping command lines
bowtie2 -x hs37m -X 650 -q -1 r1.fq -2 r2.fq -S r12.bowtie2.sam bwa aln hs37m.fa r1.fq > r1.sai && bwa aln hs37m.fa r2.fq > r2.sai \ &&am...2195 days ago
Interview Puzzles for Bioinformatician !
These are some of the most famous Interview Puzzles being asked in top tech companies.Here is a list of Top 25 puzzles which have been asked in top Tech Interview....2132 days ago
Parallel Processing with Perl !
...essor) and if we have 500 million lines in the dataset it takes more th...ve been using. I am more inclined towards using perl fork than pe...You can lock the file using flock command. open (my $QUAL, &ldquo...can use unix “split” command for thisfor example:my $nu...2093 days ago
