Currently, genomic DNA alignment of DPM reads is only performed with read 1.
If read 2 is sufficiently long to read past the barcode and into the genomic DNA sequence, then the ChIP-DIP dataset effectively contains paired-end genomic data. Such information would be useful in determining fragment lengths.
Proposal: add an option to config.yaml to decide whether to attempt paired-end alignment, and implement appropriately
Currently, genomic DNA alignment of DPM reads is only performed with read 1.
If read 2 is sufficiently long to read past the barcode and into the genomic DNA sequence, then the ChIP-DIP dataset effectively contains paired-end genomic data. Such information would be useful in determining fragment lengths.
Proposal: add an option to
config.yamlto decide whether to attempt paired-end alignment, and implement appropriately