Question: CNV, CNA and SNP calling
0
gravatar for Pin.Bioinf
6 months ago by
Pin.Bioinf250
Malaga
Pin.Bioinf250 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 • 339 views
ADD COMMENTlink modified 6 months ago by Nicolas Rosewick7.7k • written 6 months ago by Pin.Bioinf250
2
gravatar for Nicolas Rosewick
6 months ago by
Belgium, Brussels
Nicolas Rosewick7.7k wrote:

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

ADD COMMENTlink modified 6 months ago • written 6 months ago by Nicolas Rosewick7.7k

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 6 months ago by Pin.Bioinf250
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 6 months ago by WouterDeCoster39k
1

As Wouter mentioned it depends on the related biological question.

ADD REPLYlink written 6 months ago by Nicolas Rosewick7.7k

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 6 months ago • written 6 months ago by Pin.Bioinf250
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 934 users visited in the last hour