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Published 20 hours ago • verified publisher icon lh3

How does bfc assign quality scores?

Open danshu opened this issue 8 years ago • 3 comments

After error correction, I noticed that some quality scores are strange: ?????????????????????????????????????????????????????????????????????????????????????????????+????????+???????????+?????????????

danshu avatar Feb 09 '17 02:02 danshu

Phred+33 (Sanger/Illumina) regular quality values, ?=30, +=10. Looks not that strange IMHO.

sklages avatar Feb 09 '17 07:02 sklages

I checked the quality scores of 1 read before and after error correction. Before: 33AAA/FBCEGGGEFGGGGGGGGFFGF:FFFFGG>FGGGGED@1FG1=<>C/EECGGGCEGECF:FGGC@FFBFF@C<F</<0CEGFB@CG08@FGGGGGGG@GE;<F=FCG0..8@/DGG After: the header is ec:Z:0_0:2_0_1:1_0 ++???+?????????????????????????????????????+??+????+??????????????????????????????+?+??????????+?????????????"??????+++??+???

So according to the header, only 1 error was corrected in this read, but the quality scores of most bases have been changed.

danshu avatar Feb 09 '17 08:02 danshu

It seems that the quality scores of most bases were lower after error correction.

danshu avatar Feb 09 '17 08:02 danshu