Results for "nr"
Bio-Scripts
Perl script to count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence
...Cytosine = $count_of_C\n"; print "Guanine = $count_of_G\n"; print "Thymine = $count_of_T\n"; if ($errors) { print "There were $errors unrecognized bases.\n"; }2924 days ago
Transpose the file coordinates and plot dendrogram in R
#Save this as tr.awk { for (i=1; i2625 days ago
Unzip all the genome file and remove all fasta header except first one
#!/bin/bash gzip -d *.gz FILES=$(pwd)/* for f in $FILES do echo "Processing $f file..." if [[ $f =~ \.fna$ ]]; then awk ' /^>/ && FNR > 1 {next} {print $0} ' $f | s...2539 days ago
Perl script to read multi fasta sequence one by one
#!/usr/bin/env perl use strict; use warnings; #USAGE #perl rohanRun.pl seq.fa my $outfile='tmp.fa'; my $fastaSeq_ref = readfasta ("$ARGV[0]"); my %fastaSeq = %$fastaSeq_r...2229 days ago
- ...tall zsh: correct 'install' to 'INSTALL' [nyae]? n configure: WARNING: unrecognized options: --with-boos...changed config.status: executing depfiles commands configure: WARNING: unrecognized options: --with-boos...
2159 days ago
- ...s Applied to spots when --split-spot is not set, otherwise - to individual reads -M|--minReadLen Filter by s...
2134 days ago
Perl script to break the contigs by 'N'
...$seqobj->seq; my $lenseq=length $seq; $seq = uc $seq; #now all bases are in uppercase #Searches for NNNNN regions (scaffold breaks) #Hash nregions stores a hash from the...2071 days ago
Installing Platypus on Ubuntu !
.../temp.linux-x86_64-2.7/cython/htslibWrapper.o -funroll-loops -D_LARGEFILE64_SOURC...o build/temp.linux-x86_64-2.7/cython/arrays.o -funroll-loops -D_LARGEFILE64_SOURC...ix/bgzf.c.pysam.c: At top level: cc1: warning: unrecognized command line option...2027 days ago
Bash script to handle Multifasta files
...$ awk '{if ($0 ~/_/) {printf ">";} print $0; }' input.fasta > output.fasta #Match FASTA headers in two different multi-FASTA files $ awk 'NR=FNR{a[$0];next}$0 in a{print $0}'...1365 days ago
Commandline for paired end reads simulation with BBMap !
...to finish. Finished. snpRate=0.0, max=0, unique=true insRate=0.0, max=0, len=(0-0) delRate=0.0, max=0, len=(0-0) subRate=0.0, max=0, len=(0-0) nRate =0.0, max=0, len=(0-0) g...998 days ago
