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THR13_2673_S01 Sample No-Toil RNASeq

Server/Computer: courtyard

Login ID: nmohamm5

Time: 2022.06.08

NOTE: This experiment was done with the small rsem(8.8M) and star(2.0G) references found here. It should be redone with the larger references, rsem(1.1G) and star(25G).

Download THR13_2673_S01 sample data.

mkdir data2/ && cd data2/
wget https://courtyard.gi.ucsc.edu/~hbeale//THR13_2673_S01/SU-DIPG_19_S5_L001_R1_001.fastq.gz
wget https://courtyard.gi.ucsc.edu/~hbeale//THR13_2673_S01/SU-DIPG_19_S5_L001_R2_001.fastq.gz
wget https://courtyard.gi.ucsc.edu/~hbeale//THR13_2673_S01/rsem_genes.results
mv rsem_genes.results orig_rsem_genes.results

Transfer over rsem and star ref.

cp -r ../data/starIndex /
cp -r ../data/rsem_ref_hg38 /

Make star output dir inside /data2.

mkdir star

Run pipline.

docker run --rm -v /mnt/notoil_rnaseq/data2/:/data rnaseq:latest /data/SU-DIPG_19_S5_L001_R1_001.fastq.gz /data/SU-DIPG_19_S5_L001_R2_001.fastq.gz

Diff the results with the downloaded results.

diff rsem.genes.results orig_rsem_genes.results

Diff showed no differences.