Notes for Lauren
--

> Download Illumina RNAseq data

conda create -yn sra
source activate sra

conda install -yc bioconda sra-tools

mkdir $HOME/data
cd $HOME/data
prefetch SRR7874621

fastq-dump --split-files --split-spot $HOME/ncbi/public/sra/SRR7874621.sra
rm -fr $HOME/ncbi/

> Subsample the data

source activate orp

seqtk sample -s1998 SRR7874621_1.fastq 1000000 > reads.1.fq
seqtk sample -s1998 SRR7874621_2.fastq 1000000 > reads.2.fq
rm SRR1789336_*.fastq 

> Assemble using the ORP

$HOME/Oyster_River_Protocol/oyster.mk \
TPM_FILT=1 \
MEM=50 \
CPU=24 \
READ1=reads.1.fq \
READ2=reads.2.fq \
RUNOUT=SRR7874621_1M