chhylp123 / BitMapperBS

BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing
Apache License 2.0
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How should I understand 'error best_score' and 'scoreMax' ? #26

Open wy-cmd opened 6 months ago

wy-cmd commented 6 months ago

Hi, I hope this message finds you well. I am seeking your expertise regarding an issue I encountered during the alignment of my data with lambda. The process yielded the following log:

Total Time: 4066.55 No. of Reads: 731395647 No. of Unique Mapped Reads: 99374694 (13.59%) No. of Ambiguous Mapped Reads: 13881 (0.00%) No. of Unmapped Reads: 632007072 (86.41%) Mismatch and Indel Rate: 0.55%

During this process, I encountered several instances of the message 'error best_score' with varying values, such as 'error best_score: -200, scoreMax: -128' and 'error best_score: -178, scoreMax: -112' repeatedly.

May I kindly ask for your interpretation of the 'error best_score: -178, scoreMax: -112'? Does this suggest there may be an issue with my dataset? Additionally, the alignment rate was calculated to be 13.59%, which intuitively seems somewhat elevated. Could this be indicative of an underlying problem or an anomaly in the data?