search

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.
Other
131 stars 41 forks source link

WGBS/ATAC data as input for AA #114

Open juheon opened 2 years ago

juheon commented 2 years ago

Hello,

I have generated WGBS/ATAC data for my samples but no WGS data. Is WGBS/ATAC data valid input for AA? Both data are often used to infer CNV so I guess WGBS/ATAC might produce a concordant list of candidate ecDNAs compared to WGS-based analysis. Have you happened to test either WGBS/ATAC data as an alternative input for AA?

Best regards, Ju Heon Maeng

jluebeck commented 2 years ago

Hi,

Thank you for your interest. Unfortunately WGBS/ATAC are not suitable inputs for AA; only paired-end WGS is usable currently. I agree that you will likely identify concordant CNV focal amplification regions to some degree when comparing CNV calls between the different technologies.

Jens