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
OP changed title and content some time after asking this post. Here are the original title and content:
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.
