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Forum: Bioinformatics 04-15-2012, 03:37 PM
Replies: 3
Views: 8,487
Posted By mdjones66
Yeah this is driving me nuts too. Seems google...

Yeah this is driving me nuts too. Seems google only know that the question has been asked but it doesn't now the answer.
Forum: Bioinformatics 01-16-2012, 11:32 AM
Replies: 1
Views: 2,776
Posted By mdjones66
Question BWA Reports High Mapping Quality for Poorly Mapped Pairs

I realized after I, serendipitously, ran "bwa sampe" on the same identical alignments (i.e. sai files from the same fastq) that the second mate in the pair would almost always have many mismatches....
Forum: Bioinformatics 10-27-2010, 08:41 PM
Replies: 0
Views: 2,148
Posted By mdjones66
Bimodal Distribution of Mismatch Frequencies in Illumina

I created a pileup file using Maq. If I look at the log transformed distributions of frequencies of mismatch for each nucleotide across all positions,

(forward mismatch /forward depth + reverse...
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