Results for "fine 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...2297 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...2113 days ago
Long reads mapper bash script !
#!/bin/bash #only for LONG READS mapping #USAGE: runMapper.sh minimap2...echo "Name of the file used for mapping $fileName, present at $refFas...lName == "bwa" ]; then echo "Mapping with $toolName" $bwaMemLo...ame == "ngmlr" ]; then echo "Mapping with $toolName" if [ $reads...2111 days ago
- ➜ BorisTrinityAssembly /home/urbe/Tools/transrate-1.0.3-linux-x86_64/transrate...three kinds of metrics: 1. sequence based (if --assembly is given) 2. read mapping based (if --left and --right...
2112 days ago
- 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
1823 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManager; use Bio::Se...accession_number}{status} = "OK"; #everybody starts fine $sequence_data{$accession_number}{problem_desc} = "-"; #everybody starts fine...1675 days ago
Bash script to alignment of short reads against reference genome !
bwa mem -t 40 -R '@RG\tID:K12\tSM:K12' \ E.coli_K12_MG1655.fa SRR1770413_1.fas...is marks reads which appear to be redundant PCR duplicates based on their read mapping position. It uses the same cr...1548 days ago
Installing docker for Bioinformatics on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove docker docker-engine d...ause all processes within one or more containers port List port mappings or a specific mapping for the container ps...1502 days ago
- 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 samtools...
856 days ago
