BOL: Neel's wire posts

Wire post by Neel

Neel — Fri, 12 Oct 2018 07:37:52 -0500

Consensus of nucleotide sequences https://www.perlmonks.org/bare/?node_id=500962 #Consensus #Nucleotide #DNA

Wire post by Neel

Neel — Tue, 09 Oct 2018 14:35:36 -0500

PacBio data to download http://www.cbcb.umd.edu/software/PBcR/original/index.html #pacbio #data

Wire post by Neel

Neel — Mon, 01 Oct 2018 11:59:41 -0500

GATK is open source https://software.broadinstitute.org/gatk/ #GATK #Broad

Wire post by Neel

Neel — Mon, 01 Oct 2018 11:41:35 -0500

Reverse complement of fasta sequence $ tr -d "\n " < chrII.fa | tr "[ATGCatgcNn]" "[TACGtacgNn]" | rev > chrII_reverseHai.fa #Reverse #Complement #DNA

Wire post by Neel

Neel — Mon, 01 Oct 2018 09:55:38 -0500

Add some text at the beginning of the file $ echo -e "chrII_reverse\n$(cat chrII_reverse.fa )" > chrII_reverse.fa #Add #FirstLine #Text

Wire post by Neel

Neel — Mon, 01 Oct 2018 09:03:12 -0500

Multifasta to singleline fasta. $ awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa #Multi #Single #Fasta #Convert

Wire post by Neel

Neel — Fri, 20 Jul 2018 10:10:02 -0500

https://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it #VCF #vcf #SNP

Wire post by Neel

Neel — Tue, 12 Jun 2018 13:30:49 -0500

#Convert a #multi-line #fasta to a #singleline #fasta $ awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' sample1.fa > sample1_singleline.fa

Wire post by Neel

Neel — Tue, 12 Jun 2018 13:14:13 -0500

sed -i -e '/^+/,/^\@/{/^+/!{/^\@/!d}}; /^+/ d; s/@/>/g' OUTPUT.fastq > out.fa #Convert

Wire post by Neel

Neel — Sun, 06 May 2018 07:29:03 -0500

Bioinformatics Job at MDU, Rohtak http://www.mdurohtak.ac.in/pdf18/Advt/ADvertisement%2028%20of%202018.pdf #MDU #Rohtak

Wire post by Neel

Neel — Sun, 06 May 2018 07:28:19 -0500

Bioinformatics job at Naotia University https://drive.google.com/file/d/0B0Y1Fpxmzyd3OHQ3aUNYa3hZY2c/view?pref=2&pli=1 #Job #Neotia #Professor

Wire post by Neel

Neel — Thu, 01 Mar 2018 10:26:36 -0600

One the DVD tray in Ubuntu $ eject $ eject -t #Close #Tray #Ubuntu #DVD

Wire post by Neel

Neel — Thu, 21 Dec 2017 03:52:03 -0600

Bioinformatics opportunity for AU, India students http://allduniv.ac.in/ckfinder/userfiles/files/Final%20Advt%20171117.pdf #AU #Allahabad #Opportunity

Wire post by Neel

Neel — Wed, 06 Dec 2017 09:09:51 -0600

Store all files in a array using perl: my @filesbwa = <$base_name/reads/$base_name.$library.bwa.*fa> #Store #Keep #Array #Perl

Wire post by Neel

Neel — Sat, 02 Dec 2017 08:51:07 -0600

Bioinformatics JRF at IIT https://www.iitr.ac.in/administration/uploads/File/bt/2017/adv30112017.pdf #JRF