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Posts by rrdavis
... Out of the 307795 reads that map in the paired end analysis, 189907 reads have a mapQ >=5 (~61%). ...
... 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 ...
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