Question: CNV, CNA and SNP calling
0
gravatar for Pin.Bioinf
11 weeks ago by
Pin.Bioinf230
Malaga
Pin.Bioinf230 wrote:

Hello,

I have a very basic question because I have never worked with SNPS or CNVs:

If I have many tumor samples and many normal samples from different patients, am I supposed to be calling the CNVS and SNPS for each patient? Like: tumor patient 1 vs normal patient 1

Or am I supposed to compare all at the same time like in a differential expression analysis?

Thank you

snp cnv cna • 196 views
ADD COMMENTlink modified 11 weeks ago by Nicolas Rosewick7.3k • written 11 weeks ago by Pin.Bioinf230
2
gravatar for Nicolas Rosewick
11 weeks ago by
Belgium, Brussels
Nicolas Rosewick7.3k wrote:

You should compare the pair samples (tumor and control) from the same patient. Not all tum vs all control.

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by Nicolas Rosewick7.3k

Thank you! And then, what is the statistics applied to draw a conclusion from all individual comparisons? (Im not there yet, but its curiosity)

ADD REPLYlink written 11 weeks ago by Pin.Bioinf230
1

We don't know what your biological question is.

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.
Upvote|Bookmark|Accept

ADD REPLYlink written 11 weeks ago by WouterDeCoster36k
1

As Wouter mentioned it depends on the related biological question.

ADD REPLYlink written 10 weeks ago by Nicolas Rosewick7.3k

Okay. What I actually want to observe is if there is a SNP and / or CNA change in a same tumor along time. So I am using tumor at time 1 as control and tumor at time 2 as tumor in Varscan . Is that correct? Because I want to see the changes in between. Or maybe i should call for snps and cnas individually for each tumor (like varscan allows to do) and then compare both .tsv files and see if there is a difference in there.?

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by Pin.Bioinf230
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