I want to extract reads and ColorQualitys from unmapped reads of bioscope output, here is one line sample :
788_2043_1964 141 * 0 0 * * 0 0 * * RG:Z:20110319033913614 CQ:Z:%+&%%&(%()%&%&%%-).+&'2-0)%485/(%). CS:Z:G31102022112011103111111111011111111
As I guess 14th and 13th fields should be reads and quality respectively , Shouldn't it !? If so , Can you tell me why quality is not in the numeric format!?
2 answers
It's phred scale quality scores. The numeric format that the original .quals files are in takes up too much space and wouldn't fit into the .sam specifications.
These quality scores look like Sanger type phred quality scores as it includes the '%' character which is I think ascii 37.
If you really want numeric data, you'll have to convert the phred scale quality scores. You can use the python 'ord' function to get the numeric value of the ascii character. For example:
ord('%')
Would return 37. Then you just have to subtract 33 (Sanger phred scale is 33-126) from that ascii value to get the numerical score.
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