Merge pull request #116 from umccr/fix/counts-gencode39

umccr · Aug 21, 2023 · 18f35a2 · 18f35a2
2 parents c697544 + 32b975b
commit 18f35a2
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/rmd_files/RNAseq_report.Rmd b/rmd_files/RNAseq_report.Rmd
@@ -1938,7 +1938,9 @@ if ( !is.null(params$bcbio_rnaseq) ) {
   
   if ( file.exists(salmon_gene_quant_output) ) {
     counts_salmon <- read.table(paste0(dataDir, "/", list.files(dataDir, pattern=".quant.genes.sf$")), sep="\t", as.is=TRUE, header=TRUE) %>%
-    dplyr::select(Name, NumReads)
+    dplyr::select(Name, NumReads) %>%
+    dplyr::filter(!grepl('PAR_Y', Name)) %>%
+    dplyr::mutate(Name = sub("\\..*", "", Name))
   } else if ( file.exists(salmon_transcript_quant_output) ) {
     txi.salmon <- tximport(paste0(dataDir, "/", list.files(dataDir, pattern=".quant.sf$")), type = "salmon", tx2gene = tx2ensembl)