tayabsoomro

USEFUL COMMANDS FOR BIOINFORMATICS WORK

1. Converting FASTQ file to FASTA file
2. Convert SAM file to BAM
3. Sort BAM file
4. Index BAM file
5. Get subset of sequence from FASTA file
6. Get particular record from multi-FASTA file
7. Filter records based on the sequence length in FASTQ
8. Local BLAST output format options

tayabsoomro

#!/usr/bin/bash
SAM=/isilon/saskatoon-rdc/users/soomrot/genome_comparison/minimap2/run4_pbpt3.sorted.bam
TOTAL_GAP_BP=0
prev_end_ref=-404
prev_end_query=-404
prev_old_contig_name=""
PATH_TO_NEW_CONTIG_FILE=/isilon/saskatoon-rdc/users/soomrot/data/OX1905abc/OX1905-Assembly/run4/all_contigs.fasta
PATH_TO_FASTA=/home/AAFC-AAC/soomrot/software
PATH_TO_PBPT3=/isilon/saskatoon-rdc/users/soomrot/genome_comparison/nucmer_run/pbpt3.fasta

tayabsoomro

#!/bin/sh

#####################################################################
# SYNOPSIS
#	The following script was used for the shortlist of
#	the peptides sent for Arabidopsis-specific array
#	synthesis
#
# 	DAPPLE2 Configruation 
#		Target Organism 		: {ANY}

tayabsoomro