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Assessing Mapping Results
samtools view, sort, index
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Help! I have a lots of reads and a large number of reads. Make BWA go faster!
Use threading option in the bwa command ( bwa -t <number of threads>)
- Split one data file into smaller chunks and run multiple instances of bwa. Finally concatenate the output.
- WAIT! We have a pipeline for that!
- Look for runBWA.sh in $BI/bin (it should be in your path)
Now that we are done mapping, lets look at how to assess mapping results.