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