depends on #3
Update workflow/scripts/process_dexseq_tbl.R to add average TPM, PAU & delta columns to DEXSeq results table.
Details TBC.
random thought/concern - should we recalculate PAU based on expressions of filtered/assessed PAS? DEXSeq script will perform some pre-filtering (minimum expression & relative expression) on individual PAS), so PAUs calculated from QAPA output may be based on a different set of PAS for the gene than evaluated by DEXSeq. Could do it just group-wise (e.g. use the mean/median TPMs of assessed PAS to re-calculate PAUs), or alternatively use the normalised count matrix to calculate?
depends on #3
Update
workflow/scripts/process_dexseq_tbl.Rto add average TPM, PAU & delta columns to DEXSeq results table.Details TBC.
random thought/concern - should we recalculate PAU based on expressions of filtered/assessed PAS? DEXSeq script will perform some pre-filtering (minimum expression & relative expression) on individual PAS), so PAUs calculated from QAPA output may be based on a different set of PAS for the gene than evaluated by DEXSeq. Could do it just group-wise (e.g. use the mean/median TPMs of assessed PAS to re-calculate PAUs), or alternatively use the normalised count matrix to calculate?