Order of input

[ktruve]

Hi, I would like to make sure that the format of my input file is in the correct order to be analysed correctly. I used SigProfilerMatrixGenerator to produce my input file. In this file the row names describe the type of mutation. If I understand it correctly the input to FFPEsig does not need these row names, but instead have to come in a specific order. I assume the order of the mutation types in the matrix must be the same as in this file – is that correct? https://github.com/QingliGuo/FFPEsig/blob/main/Data/FFPE_signatures_96-channel.csv

Thanks!

[QingliGuo]

Yes. It is correct that FFPEsig does not read row-names as it uses the default order of the 96 mutational channels as in COSMIC, e.g. https://cancer.sanger.ac.uk/signatures/sbs/sbs1/.

You need to re-order the output file if it is generated from SigProfilerMatrixGenerator.

[ktruve]

Hi,

The COSMIC database has the same order of the 96 mutational channels as the output of SigProfilerMatrixGenerator.

I got confused since your file https://github.com/QingliGuo/FFPEsig/blob/main/Data/FFPE_signatures_96-channel.csv does not have not this order. (start to deviate at row 6)

But it is correct then that the COMIC order is correct for input to FFPEsig and not your file linked above?

I’ll attach the order that I found at COSMIC

Best,

Katarina

On 17 Jan 2023, at 18:15, QingliGuo @.***> wrote:

Yes. It is correct that FFPEsig does not read row-names as it uses the default order of the 96 mutational channels as in COSMIC, e.g. https://cancer.sanger.ac.uk/signatures/sbs/sbs1/.

You need to re-order the output file if it is generated from SigProfilerMatrixGenerator as it differs from the COSMIC database.

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Type A[C>A]A A[C>A]C A[C>A]G A[C>A]T A[C>G]A A[C>G]C A[C>G]G A[C>G]T A[C>T]A A[C>T]C A[C>T]G A[C>T]T A[T>A]A A[T>A]C A[T>A]G A[T>A]T A[T>C]A A[T>C]C A[T>C]G A[T>C]T A[T>G]A A[T>G]C A[T>G]G A[T>G]T C[C>A]A C[C>A]C C[C>A]G C[C>A]T C[C>G]A C[C>G]C C[C>G]G C[C>G]T C[C>T]A C[C>T]C C[C>T]G C[C>T]T C[T>A]A C[T>A]C C[T>A]G C[T>A]T C[T>C]A C[T>C]C C[T>C]G C[T>C]T C[T>G]A C[T>G]C C[T>G]G C[T>G]T G[C>A]A G[C>A]C G[C>A]G G[C>A]T G[C>G]A G[C>G]C G[C>G]G G[C>G]T G[C>T]A G[C>T]C G[C>T]G G[C>T]T G[T>A]A G[T>A]C G[T>A]G G[T>A]T G[T>C]A G[T>C]C G[T>C]G G[T>C]T G[T>G]A G[T>G]C G[T>G]G G[T>G]T T[C>A]A T[C>A]C T[C>A]G T[C>A]T T[C>G]A T[C>G]C T[C>G]G T[C>G]T T[C>T]A T[C>T]C T[C>T]G T[C>T]T T[T>A]A T[T>A]C T[T>A]G T[T>A]T T[T>C]A T[T>C]C T[T>C]G T[T>C]T T[T>G]A T[T>G]C T[T>G]G T[T>G]T

[QingliGuo]

Sorry for the confusion. You are right that the current COSMIC and SigProfilerMatrixGenerator outputs have the same order, the alphabet order you pasted here. (My earlier downloads go with 16 C>A mutational channels first then C>G, etc.)

Note that the input data for FFPEsig needs to be in the same order as shown in the classic 96-channel plot (16 C>A mutational channels first then C>G, etc), so please use the file I shared.