hemoglobin expression

dge_workflow/dge_analysis.R

@@ -125,7 +125,7 @@ repFpkmMatrix(genes(cuff)) %>%
     merge(geneInfo, by="ensembl_gene_id", all.x=T) %>%
     print_head() %>%
     write.delim(file="gene_fpkms_by_replicate.txt")
-# gene_fpkms <- read.delim("gene_fpkms_by_replicate.txt")
+# gene_fpkms_by_replicate <- read.delim("gene_fpkms_by_replicate.txt")
 #' [Annotated Expresssion Table](gene_fpkms_by_replicate.txt)
 
 ## also export count tables

dge_workflow/todo.txt

@@ -4,4 +4,18 @@
 
 
 1) evaluate if trimmoatic is the better trimmer (with respect to cutadapt)
-- also consider to use contamination list from fastqc for trimming (see https://www.biostars.org/p/15753/)
\ No newline at end of file
+- also consider to use contamination list from fastqc for trimming (see https://www.biostars.org/p/15753/)
+
+
+Multi-Mapper
+---
+
+
+- perl filter does not seem change tophat results
+- samtools view -bq1 removes something (nur bei tophat default "-g 20")
+- "-g1" --> no multimapper in algn_summary and not filter effect
+
+
+next:
+- are removed/remaining counts consistent with reported multimapper counts from algn_summary.txt
+- are there duplicated read ids when using -g1