Comparing Solid Data

[mdeng]

Hi Folks,

I am quite new at Bioinformatics. I just know the really basics like NW, SW, GOTOH, cluster analysis, SVM, etc.
Usually I am a regular computer scientist, with a bit of bioinformatics background.
I was asked to perform some calculations.
I have got sequenced data from:
- FFPE Tumor
- FFPE Normal
- Frozen Tumor

Our interest is to get some information about the data. We want to get a similarity score, that tells us, how similar the datasets are to each other.

All the Data we have got are reads from Exoms in .tsv files.

Maybe some of you have got some hints to get startet or some infos about tools and workflows.

With best,

Mario

P.S. I Attached the first two lines of one .tsv file, maybe its usefull.

[deksta]

De-novo alignments

Hi Mario,

I just sent you a message about FFPE samples because I've beet trying to sequence them for a while for use on Solids...

It seems to me that some kind of de-novo alignment is needed for all the samples. I'm assuming they are all from the same person? I'm not sure what packages can handle NGS scale data.

dex*

[mdeng]

Ok,

thank you. Anybody else an Idea?

[mdeng]

Allright,

now we got a first Idea:
We want to compare FFPE normal to hg19 and try to get a similarity score. If FFPE normal has high similarity to hg19, we will use FFPE as reference.
After that, compare the other samples.

Notes, memos, ideas are welcome.

With best from GER.