Using INTEGRATE to search WGS supporting reads

[heyao]

Hi Jin,

I was wondering that if I can compile a separated utility program from the source code of INTEGRATE to perform WGS reads searching if I have already got candidate fusions and supporting reads from other methods ?

In a word , I just want to run the step 8 and 9 of INTEGRATE showed in the Supplementary Figure 9 in the INTEGRATE paper by giving a candidate list of fusions and WGS bam.

Although I am not familiar with C++ , If you would like to provide a technical note of the source code describing which *.cpp files are used for step 8 and 9 and the input for them , I can try to learn how to build this utility by myself.

Thanks in advance.

Yao He

Graduate Student
Zhang Zemin’s Lab,
BIOPIC,Colleage of Life Sciences,
Peking University
Beijing,100871
China

[Jin]

The code is focusing on combining RNA-Seq and WGS data. It can also run using RNA-seq data. The function you asked that only involves WGS data has not been implemented yet.

The functions you need for step 8 and 9 are in Dna.cpp and Dna.h. But I woundn't recommend you to try and hack the code, especially when you are not familar with C++. To get to the functions in the DNA.cpp, you will have to create the required data structures and objects, which may invole some pieces pretty much from all the other classes in the code.

For you case, Instead of hack the C++ code, you may consider implement step 8 and 9 using the language you are familar with. The details of step 8 and 9 can be found in the supplemenary methods and figures.