User: rrdavis

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rrdavis20
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Posts by rrdavis

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Comment: C: BWA mem paired end vs single end shows unusual flagstat summary
... Out of the 307795 reads that map in the paired end analysis, 189907 reads have a mapQ >=5 (~61%). ...
written 4.0 years ago by rrdavis20
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BWA mem paired end vs single end shows unusual flagstat summary
... I used BWA mem to align some Miseq (2X300bp) reads to a human reference expecting very low mapping since human reads would be considered contaminants. If I map read1 only I get the following output from samtools flagstat: 238834 + 0 in total (QC-passed reads + QC-failed reads) 0 + 0 dupli ...
alignment next-gen sequencing written 4.0 years ago by rrdavis20

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Popular Question 4.0 years ago, created a question with more than 1,000 views. For BWA mem paired end vs single end shows unusual flagstat summary

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