Running novobreak on a single sample

[kalexiou]

Hi,

In the paper Novel sequences, structural variations and gene presence variations of Asian cultivated rice authors run novoBreak on each of 3,010 rice accessions independently with default parameters.

I want to ask you how is it possible to run the tool on a single sample. The bash script ./run_novoBreak.sh is asking for control and treated sample.

I have also send an email to the corresponding author of the paper, but I thought that I may get a faster response here.

Thanks!

[MateuszChilinski]

Any luck in getting the response? :)

[kalexiou]

Everything has been resolved

Thanks

El jue., 5 de diciembre de 2019 16:49, Mateusz Chiliński < notifications@github.com> escribió:

Any luck in getting the response? :)

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[MateuszChilinski]

Could you share the answer? Because I need to run it without tumor sample as well, and I have no luck in doing so :)

[kalexiou]

Hi,

You just generate a dumb control bam file from the bam of the sample.

samtools view -H sample.bam | samtools view -bh > control.bam

samtools index control.bam

Then you launch the nb_distribution.sh file with the sample and control bams.

Give it a try and let me know if it doesn't work.

Good luck!

El jue., 5 de diciembre de 2019 22:29, Mateusz Chiliński < notifications@github.com> escribió:

Could you share the answer? Because I need to run it without tumor sample as well, and I have no luck in doing so :)

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[MateuszChilinski]

Sample is used as normal bam, and the control bam is used as tumor_bam, right?

[kalexiou]

The other way around

El jue., 5 de diciembre de 2019 23:15, Mateusz Chiliński < notifications@github.com> escribió:

Sample is used as normal bam, and the control bam is used as tumor_bam, right?

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[MateuszChilinski]

Thank you a lot, I will try it as soon as I can :)