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virajbdeshpande / AmpliconArchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon. In the current version, AA takes as input next generation sequencing reads (paired-end Illumina reads) mapped to the hg19/GRCh37 reference sequence and one or more regions of interest. Please "watch" this repository for improvements in runtime, accuracy and annotations for GRCh38 human reference genome coming up soon.
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how to find breakpoint count in AA result? #146

Closed aw2222222222 closed 1 month ago

aw2222222222 commented 1 month ago

hi jluebeck,

This is the graph result file I obtained using AA. How many breakpoints does this amplicon have? Is it 12?

Forgive my low level question.

Bests, crt

jluebeck commented 1 month ago

Hi, there are two discordant edges here. Discordant edges connect non-adjacent parts of the genome. They are what would be otherwise termed as SVs.

If you run AmpliconClassifier (via AmpliconSuite-pipeline), you will get a tabular SV summary file that will better annotate the SV results.

Thanks, Jens

aw2222222222 commented 1 month ago

Thank you for your reply,

So this means that the number of breakpoints for this amplicon is 2, and in the AA result, the number of breakpoints is equal to the number of discordant edges? Am I understanding correctly?

Sorry to bother you in the evening.