From cbcd6d14782d83c1294b77ec07a8b0c93adf0ecb Mon Sep 17 00:00:00 2001 From: hmsphd-Bio Date: Wed, 4 Mar 2026 15:11:53 +0530 Subject: [PATCH] Update TxDb creation method in rnaseq_gene_level.Rmd Updated the function for creating TxDb from GFF due to deprecation in GenomicFeatures package. Added comments for using txdbmaker package for Bioc V-3.19 and higher to generate TxDb objects. --- rnaseq/rnaseq_gene_level.Rmd | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/rnaseq/rnaseq_gene_level.Rmd b/rnaseq/rnaseq_gene_level.Rmd index c7e743bb..7763787d 100644 --- a/rnaseq/rnaseq_gene_level.Rmd +++ b/rnaseq/rnaseq_gene_level.Rmd @@ -37,9 +37,16 @@ Next we create an *Rsamtools* variable which wraps our BAM files, and create a t library(Rsamtools) bam.list <- BamFileList(bam.files) library(GenomicFeatures) + # for Bioc 3.0 use the commented out line # txdb <- makeTranscriptDbFromGFF(gtf.file, format="gtf") txdb <- makeTxDbFromGFF(gtf.file, format="gtf") + +# Since the Bioc V-3.19, `makeTxDbFromGFF()` is defuncted in 'GenomicFeatures' package.The function has now moved to the 'txdbmaker' package; +#therefore, for Bioc V-3.19 and higher, use `txdbmaker::makeTxDbFromGFF()` function instead. +#library(txdbmaker) +#txdb <- makeTxDbFromGFF(gtf.file, format="gtf") + exons.by.gene <- exonsBy(txdb, by="gene") ```