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AmpliconSuite / AmpliconSuite-pipeline

A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect. Previously called PrepareAA.
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empty AA_CNV_SEEDS.bed file #24

Closed gneedle1 closed 1 year ago

gneedle1 commented 2 years ago

The program seems to run fine, but my AA_CNV_SEEDS.bed file allways comes out empty.

jluebeck commented 2 years ago

Hi,

The seeds file will be empty if there are no candidate focal amplification regions detected in your sample. If you think that occurred erroneously (that there are focal amplifications), let me know and we can determine how to debug your case.

Jens

gneedle1 commented 2 years ago

I know there is definitely a duplication of one gene, is that enough? I am just tryin to see if I can get the program to work before using actual data so this is just some test WGS I already had. Would I still be able to test run Amplicon Architect with an empty AA_CNV_SEEDS.bed file?

jluebeck commented 2 years ago

Hi, we do not consider simple gene duplication events to necessarily be focal amplifications on their own, so it is unlikely the tool would put such events into the seeds file.

Here is a good testing dataset for AA: https://www.ncbi.nlm.nih.gov/sra/SRX5055022[accn]. It is GBM39, an ecDNA+ cell-line that appeared in the Wu et al. 2019 and Turner et al. 2017 Nature publications.

Jens

gneedle1 commented 2 years ago

Okay, perfect, I will try it out. Thank you for your help!