CfDNA exercise answers: Difference between revisions
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(Created page with "'''Q1''' Using: <pre> samtools stat /data/shared/exercises/cfdna/patient_1.bam > patient1.stat samtools stat /data/shared/exercises/cfdna/patient_2.bam > patient2.stat plot-bamstats -p patient1 patient1.stat plot-bamstats -p patient2 patient2.stat firefox patient1.stat firefox patient2.stat </pre> Both peak at 168bp however patient 1) clearly has the greatest variance and has an overabundance of short DNA fragments compared to patient 2. '''Q2''' We first run: <p...") |
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Latest revision as of 18:05, 19 March 2024
Q1
Using:
samtools stat /data/shared/exercises/cfdna/patient_1.bam > patient1.stat samtools stat /data/shared/exercises/cfdna/patient_2.bam > patient2.stat plot-bamstats -p patient1 patient1.stat plot-bamstats -p patient2 patient2.stat firefox patient1.stat firefox patient2.stat
Both peak at 168bp however patient 1) clearly has the greatest variance and has an overabundance of short DNA fragments compared to patient 2.
Q2
We first run:
readCounter --window 100000 -c 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 /data/shared/exercises/cfdna/patient_1.bam > patient_1.wig readCounter --window 100000 -c 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22 /data/shared/exercises/cfdna/patient_2.bam > patient_2.wig
to get the fragment counts per 100kb window. Then:
grep -v fixed patient_1.wig |wc -l 28823
Q3
Running:
/data/shared/exercises/cfdna/plotCNV.R patient_1.wig /data/shared/exercises/cfdna/plotCNV.R patient_2.wig evince patient_1_CNV.pdf evince patient_2_CNV.pdf
Clearly shows that patient number one has a lot of alterations in terms of copy number.
Q4
Based on the plots for the fragment size distribution and copy number variations, patient 1 had lung squamous cell carcinoma and patient 2 was a healthy control.