My ever-growing list of commands that I use often enough to need to write down but not often enough that I can remember it. Maybe someone else will find it useful.
Get some data from SRA
##download the data using the stupid SRA toolkit ./prefetch -V SRR3311821 ##Extract the fastq data. I always run with --split-files even if I know it's single-end reads ~/bin/sratoolkit.2.8.1-ubuntu64/bin/fastq-dump --split-files -v SRR3311821.sra
Sorting and Indexing bamfiles for IGV
source samtools-1.3.1 samtools sort [email protected] 4 accepted_hits.bam -o accepted_hits_sorted.bam samtools index accepted_hits_sorted.bam