Want to eventually sum expression by polyA site (and perform differential transcript usage testing considering polyA sites as different transcript isoforms).
Need a script that takes merged GTF / augmented reference transcriptome as input & outputs a TSV mapping transcripts sharing poly(A) sites to the same 'polyA site ID (I propose gene_id + ). A 'window' parameter to merge closely overlapping sites (e.g. 25 nt either side) should also be used.
This output can be used with a tximport-style script to generate a DEXSeq/SatuRn ready count matrix for differential transcript usage
Want to eventually sum expression by polyA site (and perform differential transcript usage testing considering polyA sites as different transcript isoforms).
Need a script that takes merged GTF / augmented reference transcriptome as input & outputs a TSV mapping transcripts sharing poly(A) sites to the same 'polyA site ID (I propose gene_id +). A 'window' parameter to merge closely overlapping sites (e.g. 25 nt either side) should also be used.
This output can be used with a tximport-style script to generate a DEXSeq/SatuRn ready count matrix for differential transcript usage