Results for "Mapping"

Bio-Scripts

  • Create genome scaffolding with Perl

    #!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## uses pod documentation in usage code use Getopt::Long qw(:config auto_version auto_he...

    2271 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 +...indexed BAM files with BWA-mem or BWA-sampe in one go. An example call for mapping with this script is python...

    2087 days ago

  • Long reads mapper bash script !

    .../bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minima...echo "Name of the file used for mapping $fileName, present at $refFas...olName == "bwa" ]; then echo "Mapping with $toolName" $bwaMemLo...Name == "ngmlr" ]; then echo "Mapping with $toolName" if [ $reads...

    2085 days ago

  • Running Transrate !

    ...ly DESCRIPTION: Analyse a de-novo transcriptome assembly using three kinds of metrics: 1. sequence based (if --assembly is given) 2. read mapping based (if --left and --right...

    2086 days ago

  • One liner for reads mapping !

    bwa aln -t 8 targetGenome.fa reads.fastq | bwa samse targetGenome.fa - reads.fastq\ | samtools view -bt targetGenome.fa - | samtools sort - reads.bwa.targetGenome samtools index reads.bwa.targetGenome.bam

    1797 days ago

  • Bash script to alignment of short reads against reference genome !

    ...s: sambamba markdup SRR1770413.raw.sorted.bam SRR1770413.bam --- this marks reads which appear to be redundant PCR duplicates based on their read mapping position. It uses the same cr...

    1522 days ago

  • Installing docker for Bioinformatics on Ubuntu !

    ...logs Fetch the logs of a container pause Pause all processes within one or more containers port List port mappings or a specific mapping for the container ps...

    1476 days ago

  • Bowtie2 Mapping !

    bowtie2-build toy_dataset_contig_for_mapping.fasta toy_dataset_contig_for_mapping.btindex bowtie2 -x toy_dataset_contig_for_mapping.btindex -f -U toy_dataset_reads_for_mapping.fasta -S toy_dataset_mapped_species1.sam samto...

    830 days ago