CollectRnaSeqMetrics - no coding reads found
This is my code:
java -jar picard-2.8.0.jar CollectRnaSeqMetrics \ I= bam/Aligned.sortedByCoord.out.bam \ O= output.RNA_Metrics \ REF_FLAT= bam/refFlat.txt \ STRAND=NONE \ RIBOSOMAL_INTERVALS= bam/hg19.rRNA.interval_list.sam.txt
Almost all of my aligned reads are interpreted as intergenic.
I have aligned to hg19 and my refFlat.txt file is also hg19 ([http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refFlat.txt.gz
Can you please help?