With Rna-seq data I have used hisat2 for aligning reads to genome. To check the mapping percentage I used
samtools flagstat sample.sorted.bam
When I looked at few samples I see big number of reads passed and mapped.
Samples Total_reads Mapped_reads Sample1 1076.13 M reads 1035.27 M reads Sample2 1273.74 M reads 1175.18 M reads Sample3 768.89 M reads 760.35 M reads Sample4 105.84 M reads 101.81 M reads Sample5 506.19 M reads 496.32 M reads
1) Is that big number reads mapped for few samples common? Why I see very high mapping percentage? Libraries were generated with Ribosomal rna depletion kit.
2) For few samples I see almost 45k genes among 53k showing 0 read counts. Don't know why.
3) I would also like to check reads mapped to ribosomal genes or ribosomal RNA's. Map I know how to check that?