I have RNAseq data from cell lines measure at 5 different timepoints, and each timepoint with a biological replciate. They have been sequenced strand specifically. I align them using
hisat against ensemble built 75 with
--rna-strandness R. After, I get the raw counts with
-m union and
-s yes. I normalized the counts using TPM measurement.
As you can see, there are 3 big outliers. These three are found in all of the samples and are all misc non coding RNAs
ID counts TPM
ENSG00000258486 153195 227942.04 RN7SL1
ENSG00000265150 100826 151541.60 RN7SL2
ENSG00000202198 112308 151407.64 RN7SK
Am I doing something wrong with my alignment or counting?