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| What do you think the 4th and 8th columns mean?If you thought the answer was the mapping coordinates of the read pairs you were right! |
More reading about SAM files
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In the bowtie2 example, we mapped in
--localmode. Try mapping in--end-to-endmode (aka global mode).- Do the BWA tutorial so you can compare their outputs.
- Did bowtie2 or BWA map more reads?
- In our examples, we mapped in paired-end mode. Try to figure out how to map the reads in single-end mode and create this output.
- Which aligner took less time to run? Are there any options you can change that:
- Lead to a larger percentage of the reads being mapped? (increase sensitivity)
- Speed up performance without causing many fewer reads to be mapped? (increase performance)
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