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| Tip |
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If you're mapping to a non-genomic reference such as miRBase miRNAs or another set of genes (a transcriptome), samtools idxstats gives you a quick look at quantitative alignment results. |
Exercise #3:
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PE alignment with BioITeam
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scripts
Now that you've done everything the hard way, let's see how to do run an alignment pipeline using a BWA alignment script maintained by the BioITeam, /work2/projects/BioITeam/common/script/align_bwa_illumina.sh. Type in the script name to see its usage.
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