Results for "B"
Bio-Scripts
Perl script to count the number of files in a directory with regex
#!/usr/bin/perl use strict; use warnings; my @allNames=("_D14_","_B14_","_B15_","_C1T1_","_C3T3_","_D12_","_D13_","_E1B1_","_E1B3_","_H001_","_H3-03_...C1T2_","_D11_","_E11_","_E31_","_B11_","_B33_","_B3B1_","_C210_"..._D23_","_D21_","_A16_","_A17_","_B24_","_A3B1_","_C2B4_","_B22_"...2284 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 m...t open the file $outfile $!"; print OUT "$key\n$fastaSeq{$key}\n"; } sub readfasta { (my $file)=@...2268 days ago
- zero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4==0 {bpCountZero+=($3-$2)} {print bpCountZero}' | tail -1) nonzero=$(bedtools genomecov -ibam BAM -g hg38.fasta -bga | awk '$4>0 {bpCountNonZero+=($3-$2)} {print bpCountNonZero}' | tail -1) percent=$(bc
2257 days ago
- # get total number of bases covered at MIN_COVERAGE_DEPTH or higher samtools mpileup mapping_result_sorted.bam | awk -v X="${MIN_COVERAGE_...wc -l 32876 # get length of reference genome bowtie2-inspect -s refgenome |...
2257 days ago
Bash script to convert SAM to BAM visualization ready
samtools view -bS file.sam | samtools sort - file_sorted samtools index test_sorted.bam test_sorted.bai2230 days ago
Biological Sequence handling with Perl !
...=> 'concatenate', 'fallback' => 'TRUE'; # These methods should be overriden by child classes...er and return the result sub concatenate { my $self = s...= *reversec = \&reverse; sub new { my $class = shift;...h-$pos-3*length($max)); } sub align { my $self = shift...2228 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [u...->[0])) { while () { chomp; if (substr($_, 0, 1) eq '>' || substr...0] = undef; while () { chomp; $c = substr($_, 0, 1); last if ($c...2201 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number of input arguments is lower...e filenames my $filecodontable = $ARGV[0]; my $filesequen...he file $filesequence can not be opened\n"; exit(1); }...lations involving # small numbers between 0 and 1. Log of th...2202 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be used to obtain such files. Read pa...SST provides a script (https://github.com/ksahlin/BESST/blob/master...thon reads_to_ctg_map.py /path/to/lib1_A.fq /path/to/lib1_B.fq /pat...2171 days ago
- ...aster) ✗ git clone git://github.com/bcgsc/bloomfilter.git Cloning...ing for style of include used by make... GNU checking depend...-pc-linux-gnu checking for a BSD-compatible install... /usr/...handles long lines and -e... /bin/grep checking for egrep......
2198 days ago
