The way to interpret the results is Read counts in for the features = 36787 Now I can use information in gene_biotype "protein_coding" to add all the read count to find number of reads falls into different type of features. In order to calculate number of reads does not mapped to any features, do I just need calculate by subtracting total numbers of reads falls into different features from number of mapped read?
EDIT by @RamRS
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unmapped reads in FFPE samples
I am working with RNAseq data from FFPE samples(human). the problem is that almost half of the reads can not be mapped to human genome meaning I will loose many reads and that would have negative effect on the gene expression analysis. would you please help me to find out what the problem could be? and also is there any way to use the unmapped reads? the read length before trimming is 150 nt.
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Which tool did you use for mapping ?
bowtie and once STAR.
bowtie is a not a splice aware aligner ; thus will miss alignment of reads spanning exon-exon junctions. Use STAR 2-pass mode with ENSEMBL or Gencode annotation file and report the Log.final.out file here. If you still see low mapping rate it can be interesting to check RNA biotype distribution if you see maybe high rate of rRNA -> check here : How to calculate distribution of mapped read over classes of RNA?
RNA is expected to be fragmented with FFPE samples. There is not much you can do if your have reads that are too short to be uniquely mapped. You could try switching to
salmonto see if that helps.