HW 5 - Solution Set

HW 5.1 – Anscombe’s Quartet

See this IPython Notebook: hw5-quartet-solutions.

HW 5.2 – variant calling

To calculate the variants for the evolved set, just replace SRR098042 with SRR098038 in all of the variant calling commands:

cd /mnt
curl -O ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR098/SRR098038/SRR098038.fastq.gz
bwa aln REL606.fa SRR098038.fastq.gz  > SRR098038.sai
bwa samse REL606.fa SRR098038.sai SRR098038.fastq.gz > SRR098038.sam
samtools import REL606.fa.fai SRR098038.sam SRR098038.bam
samtools sort SRR098038.bam SRR098038.sorted
samtools index SRR098038.sorted.bam
samtools mpileup -uD -f REL606.fa SRR098038.sorted.bam | bcftools view -bvcg - > SRR098038.raw.bcf
bcftools view SRR098038.raw.bcf > SRR098038.vcf

You now have the variants in the original data set (SRR098042.vcf) and the evolved data set (SRR098038.vcf).

Let’s look at them in a little more detail: see hw5-variant-solutions.ipynb.

HW 5.3 – mRNAseq differential expression

See this notebook: hw5-mrnaseq-solutions.