BOL: Shruti Paniwala's wire posts

Wire post by Shruti Paniwala

Shruti Paniwala — Thu, 11 May 2017 14:09:42 -0500

Chi squared test https://edwards.sdsu.edu/research/calculating-chi-squared-wiht-perl/ #Perl #Chi #Probability

Wire post by Shruti Paniwala

Shruti Paniwala — Wed, 19 Apr 2017 16:44:53 -0500

Data structure with R http://staff.washington.edu/jon/dsa-perl/dsa-perl.html #R #Data #Structure #Script #Perl

Wire post by Shruti Paniwala

Shruti Paniwala — Wed, 19 Apr 2017 16:38:22 -0500

Interesting PPT on cancer genomics https://www.genome.gov/multimedia/slides/genomicsinmedicine2013-2014/helman_6-7-2013.pdf

Wire post by Shruti Paniwala

Shruti Paniwala — Thu, 16 Mar 2017 01:28:38 -0500

BioStats with R https://cran.r-project.org/doc/contrib/Seefeld_StatsRBio.pdf #R #BioStats #Example

Wire post by Shruti Paniwala

Shruti Paniwala — Thu, 09 Mar 2017 17:39:59 -0600

Online free programming books https://github.com/vhf/free-programming-books/blob/master/free-programming-books.md

Wire post by Shruti Paniwala

Shruti Paniwala — Thu, 09 Mar 2017 17:01:06 -0600

Essential perl http://cslibrary.stanford.edu/108/EssentialPerl.html

Wire post by Shruti Paniwala

Shruti Paniwala — Wed, 01 Mar 2017 17:55:34 -0600

Remove all blank lines from file. perl -i.bak -n -e "print if /\S/" ../finalSample.fa #Perl #Tricks #PerlOneliner

Wire post by Shruti Paniwala

Shruti Paniwala — Mon, 20 Feb 2017 06:07:54 -0600

Check out the OS type: $ cat /etc/*-release #Linuxv #OS

Wire post by Shruti Paniwala

Shruti Paniwala — Mon, 13 Feb 2017 06:04:35 -0600

Extract values : cat seeALN.xls | grep -w "scaffold_1" to #grep #exact #matching words from file seeALN.xls

Wire post by Shruti Paniwala

Shruti Paniwala — Mon, 23 Jan 2017 05:01:08 -0600

Fasta sequence length: awk '/^>/ {if (seqlen){print seqlen}; print ;seqlen=0;next; } { seqlen += length($0)}END{print seqlen}' file.fa #Length #Linux #OneLiner

Wire post by Shruti Paniwala

Shruti Paniwala — Tue, 22 Nov 2016 04:33:45 -0600

Extract ten lines below matched string with grep: grep -A 10 "string" filename1 ; -B for above and -C for both #grep #Linux #Tricks #Lines #Matches

Wire post by Shruti Paniwala

Shruti Paniwala — Wed, 26 Oct 2016 12:43:58 -0500

Slice on the fly with perl: my ($username, $real_name) = (split /:/, $str)[0, 4]; #Perl #PerlTrick #Split

Wire post by Shruti Paniwala

Shruti Paniwala — Wed, 26 Oct 2016 11:22:55 -0500

Re-install perl in Ubuntu: sudo aptitude reinstall perl #Perl #Ubuntu #Install #Linux

Wire post by Shruti Paniwala

Shruti Paniwala — Wed, 26 Oct 2016 09:24:08 -0500

Extract a fasta sequence from multifasta file: samtools faidx multitest.fa and then samtools faidx multitest.fa fasta_id > out.fa #Samtools #Fasta #Extract #Multifasta

Wire post by Shruti Paniwala

Shruti Paniwala — Tue, 25 Oct 2016 05:25:43 -0500

Coverage R Plot http://davetang.org/muse/2013/09/07/creating-a-coverage-plot-in-r/ #R #Plot #Genome #Image #NGS #BAM