Input format for ABSOLUTE using sequencing data

[罗思圆]

Hello,

Can anyone explain how to use ABSOLUTE for cancer DNA sequencing data? I
searched for

http://www.broadinstitute.org/cancer/cga/absolute_run

But did not find enough information. Specifically, ABSOLUTE requires the
input data to have at least four columns:
"Chromosome", "Start", "End", "Num_Probes" and "Segment_Mean".

For my sequencing data, I have done the segmentation already, and I have
"Chromosome", "Start", "End", plus the number of reads mapped to the
segment in tumor sample "d_T", and the number of reads mapped to the
segment in matched normal sample "d_N". So, I'm wondering how to convert
these "d_N", "d_T" into "Num_Probes" and "Segment_Mean" for ABSOLUTE?

Thanks so much!

[GenePattern Help Forum]

Hello, 

The URL you are looking for has changed. The archived CGA site for ABSOLUTE is here:  https://software.broadinstitute.org/cancer/cga/absolute_run 

You probably need to run HAPSEG first -  https://software.broadinstitute.org/cancer/cga/hapseg_run 

We hope this helps!

Best

-Barbara 

[罗思圆]

Hi Barbara,

Thank you so much for the prompt reply!

I've read the website you mentioned as well, and it says without using HAPSEG, I can also supply a tab delimited segmentation file to ABSOLUTE as input. It's necessary for me because I'm testing my tool for segmentation as well. Now I'm still confused about what  "Num_Probes" and "Segment_Mean" should be for sequencing data. I would be really appreciate for your answer!

Best,

Siyuan

在 2020年3月6日星期五 UTC+1下午7:52:54，GenePattern Help Forum写道：