unmapped output of the STAR

Question

[Wakala]

Hello, everyone. When i use star to align the RNA seq date to human genome, the output of the unmapped.out.mate is always large, nd it unique mapped is about 70%. Is it normal?

STAR
--genomeDir $index
--genomeLoad NoSharedMemory
--runThreadN $4
--sjdbOverhang 99
--sjdbGTFfile $gtf
--alignIntronMin 20
--alignSJoverhangMin 8
--alignSJDBoverhangMin 1
--alignIntronMax 1000000
--alignMatesGapMax 1000000
--twopassMode Basic
--quantMode GeneCounts
--runMode alignReads
--readFilesCommand zcat
--readFilesIn $2/$id.fastq.gz
--outSAMunmapped None
--outSAMattributes All
--outFilterType BySJout
--outReadsUnmapped Fastx
--outFilterMultimapNmax 1
--outFilterMismatchNmax 999
--outFileNamePrefix $3/$id
--outSAMstrandField intronMotif
--outFilterMismatchNoverLmax 0.04
--outSAMtype BAM SortedByCoordinate

[lieven.sterck]

what kind of RNAseq data are you aligning? (blood sample? stool sample? ... )