Results for "DU"
Bio-Scripts
Finding Kmers from fasta sequence file
Save it in sample.fa >test TAATGCCATGGGATGTT jellyfish count -m 3 -s 100000 sample.fa -o sample.jf jellyfish dump -c sample.jf It return TGT 1 GAT 1 GGG 1 GGA 1 CAT 1 TGC 1 TAA 1 GCC 1 CCA 1 GTT 1 TGG 1 ATG 3 AAT 11974 days ago
- my @tests = ( ["FOO", "BAR"], ["CRATE", "TRACE"], ["CRATE", "CRATE"], ["TRACE", "CRATE"], ["CREATE", "TRACT"], ["DWAYNE", "DUANE"], ); for my $word_pair (@tests) {...
1802 days ago
- # $1 = vcf file # $2 = input bam file # $3 = output QV file module load samtools NUM_BP=`samtools depth $2 | perl -e '$c = 0; while(){chomp; @s = split(/\t/); if(scalar(@s)...
1606 days ago
Samtools commands for bioinformatician !
...put it into a txt file # -a : at all positions samtools depth -a sorted_dupremoved.bam > depth.txt ### one liner to count mean depth samtools depth -a sorted_dupremoved.bam | awk '{c++;s+=$3...1605 days ago
Perl script to remove duplicated lines !
#!/usr/bin/perl use strict; use warnings; { $_ = ; my $next_line; while( $next_line = ) { #print "current line: $_ -- next line: $next_line$/...1562 days ago
Bash script to download SRA file !
...(in paired FASTQ format) from the archive. fastq-dump is in the SRA toolkit. It a...ata from a particular sequencing run ID fastq-dump --split-files SRR1770413...un/sra/SRR/SRR177/SRR1770413/SRR1770413.sra sra-dump --split-files SRR1770413.sr...1561 days ago
Bash script to alignment of short reads against reference genome !
...sambamba sort SRR1770413.raw.bam sambamba markdup SRR1770413.raw.sorted.bam SR...M file, writing it to .sorted.bam. #marking PCR duplicates: sambamba markdup SRR...position. It uses the same criteria for marking duplicates as picard. minimap...1561 days ago
Bash commandline to install Anaconda !
...nstallation finished. Do you wish the installer to initialize Anaconda3 by running conda init? [yes|no] [no] >>> yes WARNING: The conda.compat module is deprecated and will be r...1557 days ago
- ...e-expansion node-builtin-modules node-combined-stream node-...universe amd64 node-builtin-modules all 1.1.1-1 [3,338 B] Get...lected package node-builtin-modules. Preparing to unpack .../..... Setting up node-builtin-modules (1.1.1-1) ... Processing...
1555 days ago
Perl script to delete the adjacent repeats !
...ernatively, if you want to ignore case when comparing, you could use: $string =~ s/(.)\1/$1/gi #And finally, if you wanted to trim any number of duplicates down to a single lett...1552 days ago
