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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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Some question about {out}_amplicon{id}_graph.txt output #73

Closed zhang919 closed 4 years ago

zhang919 commented 4 years ago

Dear， I am currently applying AA to some data and got some interesting output. I noted the output files named as {out}_amplicon{id}_graph.txt. You described this file in detail in the Readme file, In particular, there is such a statement about the position of the chromosome： {STRAND}: +/'. +/- indicates that the participating segment ends on the right or begins on the left of the corresponding basepair respectively. I don't quite understand this content, Is this equal to the distinction between positive and negative chains or I can understrand as the "+" equals "start" and the "-" equals "end"? Could you please give me more details. Thank you very much.

virajbdeshpande commented 4 years ago

Hi, I had missed this question. "-" indicates start of the segment and "+" indicates end of the segment.