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shotgun sequencing Data compatibility #15
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Hi Krunal, You should be able to use ichorCNA for your data. You do not need matched normals to analyze your samples. Best, |
Dear Gavin,
Regards |
Hi Krunal,
|
Hi Gavin, Please check the below link as requested in respect of CNA FPs. Regards |
Hi Gavin,
Is there any way to identify our baseline (healthy samples) data
properly normalized or not, as well as would like to know is there any
graph or any additional file to find the normalization status.
Please check the attached PDF as requested in respect of CNA FPs.
waiting for the reply.
Regards
Krunal
…On Thursday 29 March 2018 08:52 PM, Gavin Ha wrote:
Hi Krunal,
1.
15 normal samples is a good start. The way that the PoN is used
isn't sophisticated at the moment. More samples could help but it
may not make a dramatic difference.
2.
Are you wondering whether the predicted CNAs are false positives
and how you should filter them? It's a little bit difficult to
answer this question because I am not sure what are FPs in your
data. Do you have an example (i.e. plots)?
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Regards
Krunal Pawar
Bioinformatics Department
Datar Genetics Limited
|
Hi Krunal,
Sorry for the delay.
Looking at the profile in the PDF that you attached, it looks like there
are clearly copy number alterations. One thing I can bring up is that
perhaps it is a female sample because chromosome X is at the same level as
other chromosomes and that this sample may have experienced genome double
(ploidy should be higher). In this case, I'm not sure if the technical data
normalization is the problem. I think it may have to do with the actual
signals in your sample.
Is this sample definitely from a healthy donor or matched normal sample?
Your question regarding proper normalization - the best way is to test
ichorCNA on your data on more expected healthy/normal samples.
Hope this helps,
Gavin
|
Hi,
We have sequenced data (from Ion Torrent) for Low-pass shotgun sequencing. Is shotgun sequencing data compatibility to run ichorCNA to estimate the tumor fractionas as well as copy number identification.
If yes, can you please guide me how to create a baseline and how many normal (healthy) samples are required for the same.
Regards
Krunal
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