Results for "short reads mapping"
Bio-Scripts
Bash script to alignment of short reads against reference genome !
...s says "align using so many threads" and also "give the reads the...: samtools view -b - --- this reads SAM from stdin (the - specifi...uplicates based on their read mapping position. It uses the same...ll tell it we're working with short read data using -ax sr:1573 days ago
To convert just one specific read group to fastq
# Stop script on error. set -uex # The SRR BioProject number for the sequencing...d -$N > selected.txt # Store the data in the reads folder. mkdir -p reads # Download the SRR data fo...ll.bam # Reverting the process is to extract reads,...1556 days ago
Installing docker for Bioinformatics on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove docker docker-engine d...use all processes within one or more containers port List port mappings or a specific mapping for the container ps...1527 days ago
Perl script to reads and extract webpage contents !
use 5.010; use strict; use warnings; use WWW::Mechanize; my ($url) = @ARGV; die "Usage: $0 URL\n" if not $url; my $w = WWW::Mechanize->new; $w->get($url); say $w->content; #Run #jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ perl web.pl https://bioinformaticsonline.com1527 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-Pro-3335-MT:~/Downloads...maticsonline.com/snippets/view/41440/perl-script-to-reads-and-extract-webpage-contents...valuation of genome assembly software based on long readsBy...1525 days ago
picard tools command to get some insert statistics
#picard tools to get some insert statistics to see whether our reads seem to be in the correct place #module load picard/2.0.1 java -Xmx16g -XX:PermSize=8g -jar $PICARD_HOME/picard....1351 days ago
- (JitMetaENV) ➜ fastQC_out trimmomatic SE -phred33 SRR5322499_1.fastq out.trimmed.fastq LEADING:3 TRAILING:3 SL...LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 Automatically using 1 threads Input Reads:...
1230 days ago
- Use pen and paper the assemble it. If you are brave enough, you can try to assemble this set of reads:...
1229 days ago
Download minikraken database !
(JitMetaENV) ➜ day3 curl -O ftp://ftp.ccb.j...01904_UPDATE/hash.k2d #Check for pe reads #kraken2 --use-names --threads 4 --db minikraken2_v2_8GB_201...rt evol1 --gzip-compressed --paired ../mappings/evol1.sorted.unmapped.R1.fastq.gz ../mappings/evol1.sorted.unmapped.R2.fas...1228 days ago
- #Long reads bedtools bamtofastq -i input.bam -fq output.fastq #For paired-end reads: samtools sort -n input.bam -o input_sorted.bam # sort reads by identifier-name (-n) bedtools bamtofastq -i input_sorted.bam -fq output_r1.fastq -fq2 output_r2.fastq
1010 days ago
