https://teaching.healthtech.dtu.dk/22126/index.php?action=history&feed=atom&title=CfDNA_exercise_answers 2026-05-04T03:48:49Z Revision history for this page on the wiki MediaWiki 1.41.0 https://teaching.healthtech.dtu.dk/22126/index.php?title=CfDNA_exercise_answers&diff=75&oldid=prev 2024-03-19T16:05:43Z

<p>Created page with &quot;&#039;&#039;&#039;Q1&#039;&#039;&#039; Using: &lt;pre&gt; samtools stat /data/shared/exercises/cfdna/patient_1.bam &gt; patient1.stat samtools stat /data/shared/exercises/cfdna/patient_2.bam &gt; patient2.stat plot-bamstats -p patient1 patient1.stat plot-bamstats -p patient2 patient2.stat firefox patient1.stat firefox patient2.stat &lt;/pre&gt; Both peak at 168bp however patient 1) clearly has the greatest variance and has an overabundance of short DNA fragments compared to patient 2. &#039;&#039;&#039;Q2&#039;&#039;&#039; We first run: &lt;p...&quot;</p> <p><b>New page</b></p><div>&#039;&#039;&#039;Q1&#039;&#039;&#039;<br /> <br /> Using:<br /> <br /> &lt;pre&gt;<br /> samtools stat /data/shared/exercises/cfdna/patient_1.bam &gt; patient1.stat<br /> samtools stat /data/shared/exercises/cfdna/patient_2.bam &gt; patient2.stat<br /> <br /> plot-bamstats -p patient1 patient1.stat<br /> plot-bamstats -p patient2 patient2.stat<br /> <br /> firefox patient1.stat<br /> firefox patient2.stat<br /> <br /> &lt;/pre&gt;<br /> <br /> Both peak at 168bp however patient 1) clearly has the greatest variance and has an overabundance of short DNA fragments compared to patient 2.<br /> <br /> &#039;&#039;&#039;Q2&#039;&#039;&#039;<br /> <br /> We first run:<br /> &lt;pre&gt;<br /> 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 &gt; patient_1.wig <br /> 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 &gt; patient_2.wig <br /> &lt;/pre&gt;<br /> <br /> to get the fragment counts per 100kb window. Then:<br /> <br /> &lt;pre&gt;<br /> grep -v fixed patient_1.wig |wc -l <br /> 28823<br /> &lt;/pre&gt;<br /> <br /> &#039;&#039;&#039;Q3&#039;&#039;&#039;<br /> <br /> Running:<br /> &lt;pre&gt;<br /> /data/shared/exercises/cfdna/plotCNV.R patient_1.wig <br /> /data/shared/exercises/cfdna/plotCNV.R patient_2.wig <br /> evince patient_1_CNV.pdf<br /> evince patient_2_CNV.pdf<br /> &lt;/pre&gt;<br /> <br /> Clearly shows that patient number one has a lot of alterations in terms of copy number.<br /> <br /> &#039;&#039;&#039;Q4&#039;&#039;&#039;<br /> <br /> 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.</div>

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