About GenomonSV Merge

[GSMengyueZheng]

I don't understand the details of "control_info.txt" in step "Genomon merge". Would you mind giving me an example? When I put a "control_info1.txt", there is not a result and it shows an error of "no such file or directory: PC.junction.clustered.filt6.bedpe.tmp.tumor.psl". When I put a "control_info2.txt", there is no error, but I couldn't find any fusions in my "PC.genomonSV.result.txt". There are some fusions in the PC sample, and we have identified them using an experiment. I am appreciated for your reply, thank you!

control_info1.txt:
control NC

control_info2.txt:
control NC
tumor PC

[friend1ws]

Hi, sorry for the late response, and thank you very much for your interest in GenomonSV.

when you performed GenomonSV parse, for control_NC1 and contron_NC2, then probably you will have the data such as control_NC1.junction.clustered.bedpe.gz and control_NC2.junction.clustered.bedpe.gz.

Next, please generate the whose name is control_info.txt e.g.,
"""
control_NC1 {path to}/control_NC1.junction.clustered.bedpe.gz
control_NC2 {path_to}control_NC2.junction.clustered.bedpe.gz
"""

And performGenomonSV merge control_info.txt merge_control.bedpe.gz.
Then, please use this file to GenomonSV filt step.

Please let me know if you have any further questions.
We will try to brush up the documents...