FAQ#510 Version3
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How many mismatches are allowed for mapping the reads against the human genome?
| Category: | smallRNA Pipeline | Difficluty: |  |
| Assigned to: | - | Due date: | |
| Related issue: | - | Related Message: | - |
| Related version: | - | Valid: | Valid |
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 Bowtie 1 is 1.
For further information on default settings used by sRNAbench,
please refer to the sRNAbench manual.