I've been exploring some sequence data from SOLiD and have used Bowtie. When I was exploring the alignment, this was the ASCII-encoded read quality for one of the reads:
WYQPMQZ<8SF@NNDDLIIIINR@&9OOMA@8/BEF526+8HI<<+1J
When I convert this back to the qual score, it looks more like
54 56 48 47 44 48 57 27 23 50 37 31 45 45 35 35 43 40 40 40 40 45 49 31 5
24 46 46 44 32 31 23 14 33 36 37 20 17 21 10 23 39 40 27 27 10 16 41
However, in the .qual file, for that read, the quality score was
25 25 29 27 21 26 18 30 27 -1 23 27 10 21 24 21 14 21 22 18 22 18 22 23 26 5 -1 24 22 24 20 12 19 4 10 23 13 24 4 21 -1 10 13 26 14 13 14 4 20 21
Apologies if this question has been asked before, but why does it appear that the ASCII-encoded scores are much higher than what is in the .qual file. Does this have something to do with Bowtie?
WYQPMQZ<8SF@NNDDLIIIINR@&9OOMA@8/BEF526+8HI<<+1J
When I convert this back to the qual score, it looks more like
54 56 48 47 44 48 57 27 23 50 37 31 45 45 35 35 43 40 40 40 40 45 49 31 5
24 46 46 44 32 31 23 14 33 36 37 20 17 21 10 23 39 40 27 27 10 16 41
However, in the .qual file, for that read, the quality score was
25 25 29 27 21 26 18 30 27 -1 23 27 10 21 24 21 14 21 22 18 22 18 22 23 26 5 -1 24 22 24 20 12 19 4 10 23 13 24 4 21 -1 10 13 26 14 13 14 4 20 21
Apologies if this question has been asked before, but why does it appear that the ASCII-encoded scores are much higher than what is in the .qual file. Does this have something to do with Bowtie?
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