I used featureCounts of Rsubread and found something that I cannot explain:
I wanted to count the features in this region chr1:3044014-3044814, strandSpecific parameter was set to 0.
Somehow I do not understand how the read ...4974:39966 got into the results. Neither its end, nor its starts lie in the specified region.
If I set the strandSpecific parameter to 1. This read does not appear in the results.
HWI-ST227:372:C3UVCACXX:3:1113:4974:39966 16 chr1 3043884 255 50M * 0 0 CTGAGAGCTTGGCGCGCTGTCTCTGCAGCATAGGGGCACTAACTATGCCCJJJJJJIJJJJJJJJJJJJJJIJJJIJJJJJJJJJJJHHHHHFFFFFCCC XA:i:0 MD:Z:50 NM:i:0 HWI-ST227:372:C3UVCACXX:3:1212:16462:69280 0 chr1 3044215 255 50M * 0 0 TCCAAGATTGGTGCCGAGCCCTATTGGCCCAAGTTAGAAGTAGACATCTGCCCFFFFFHHHHHJJJJJIJJJJJIGGJJJJJJHHIIJHIBFHIJJJIIG XA:i:0 MD:Z:50 NM:i:0