reconstructCDS: Reconstruct CDS with alternative internal and downstream...
In fursham-h/ponder:

This function will add alternative segments from a query transcript into a reference CDS from the same gene and generate a new ORF

Note: This function will not insert/remove first exons.

reconstructCDS(
  queryTranscript,
  refCDS,
  fasta,
  txrevise_out = NULL,
  gene_id,
  transcript_id
)

`queryTranscript`	A GRanges object containing exon structure of a query transcript from the same gene family
`refCDS`	A GRanges object containing CCDS information of a gene family
`fasta`	Fasta sequence of the genome
`txrevise_out`	Optional. GRangesobject from 'indentifyAddedRemovedRegions()' or 'testTXforStart()' output. ?indentifyAddedRemovedRegions or ?testTXforStart for more information. Arguments refCDS and queryTranscript is not mandatory if this argument is provided

A list containing: (1) A GRanges Object of new ORF, or NA if no ORF is found (2) TRUE/FALSE object on whether ORF is an alternative CDS transcript

Fursham Hamid

1 2	library("BSgenome.Mmusculus.UCSC.mm10") reconstructCDS(ptbp2Data$transcripts$ENSMUST00000197833, ptbp2Data$refCDS, fasta = BSgenome.Mmusculus.UCSC.mm10)