FAQ#510 Version1
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How many mismatches are allowed for mapping the reads against the human genome?
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Answer
The smallRNA-seq pipeline uses the sRNAbench tool to align reads to the human genome.
sRNAbench uses a default setting noMM=1, which means the number of mismatches
used by bowtie1 is 1
For further information on default settings used by sRNAbench,
please refer to the sRNAbench manual