CollectRnaSeqMetrics - no coding reads found

Hello,

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?

Thanks!

Answers

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