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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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RNA-seq data as the input for AA #122

Closed EunchongHuang closed 2 years ago

EunchongHuang commented 2 years ago

Hello,

I have couple of RNA-seq data from TCGA and wondering if AA can take RNA-seq data (bam) as the input. Have you happened to test either RNA-seq data as an alternative input for AA?

jluebeck commented 2 years ago

Hi,

Unfortunately AA will fundamentally not work with RNA-seq data as input, sorry.

Jens