Dear All,
I am interested in calculating the % of reads associated to globin gene and rRNA genes. Right now, I am not sure whether my paired end RNAseq data has followed strand specific protocol or not. I requested the incharge person to inform me.
Meanwhile, I selected all the three options for strandedness (no,yes,reverse) in htseq-count.
How do I get the strand (sense,antisense) information
How to interpret the Stranded:Reverse counts
Globin genes | Stranded:No | Stranded:Yes | Stranded:Reverse |
HBB | 40204 | 40197 | 7 |
HBA1 | 38811 | 38795 | 16 |
HBA2 | 129847 | 129770 | 77 |
HBG1 | 1566 | 1566 | 0 |
HBG2 | 2750 | 2750 | 0 |
HBD | 3 | 3 | 0 |
HBE1 | 1 | 0 | 1 |
HBZ | 0 | 0 | 0 |
HBQ1 | 9 | 3 | 6 |
MB | 4 | 0 | 4 |
CYGB | 294 | 2 | 354 |
NGB | 289 | 2 | 319 |
How to interpret the difference among these three options
Stats from special counters
Special counters | Stranded:No | Stranded:Yes | Stranded:Reverse |
__no_feature | 56289350 | 94180089 | 56914563 |
__ambiguous | 625347 | 18161 | 343824 |
__too_low_aQual | 0 | 0 | 0 |
__not_aligned | 0 | 0 | 0 |
__alignment_not_unique | 30631662 | 30631662 | 30631662 |