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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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Chromosome Coordinate on the amplicon cycles is 1 bp less than the real genome coordinate #144

Open JungnamChoLab opened 3 months ago

JungnamChoLab commented 3 months ago

Hi there,

I have examined the junction sites of ecDNA cycles using SVABA. However, I have encountered an issue where some junction sites cannot be reassembled by SVABA. Upon further analysis, I have noticed that for the junctions detected, many of them have a 1 base pair difference compared to the real genome coordinate. I am uncertain whether this discrepancy is due to the format of the bed files or some other reasons. Does anyone have any insights or ideas?

Bests, Ling

jluebeck commented 3 months ago

Hi - thanks for reaching out.

Do you have any suggestions for how we can replicate this issue? Is there a publicly-available sample we can compare with?

Are you working with outputs from AA or from AmpliconClassifier (AC)? Keep in mind that AA's graph & cycles file are both 0-based coordinates and fully closed intervals. However, I don't see in the SVABA Readme if they are 0 or 1 based.

AC on the other hand reports using a 0-based, half-open counting system like UCSC.

Thanks, Jens

JungnamChoLab commented 3 months ago

Hi Jens,

Thank you so much for giving me answers! I think you fully addressed my second question. I worked with the output from AC. For the first issue, I worked with a not yet public dataset. But you gave the idea that I should compare with a public dataset. I will try and see.

Bests and Thanks, Ling