Evaluating mapping results
Once you've received mapped your NGS data, it is prudent to check/validate the data before investing time in analysis. Over time, you can develop quite extensive QC measures; they may be based on tools like the popular fastqc tool and samstat tools - it they can report quality value distributions, look for erroneously abundant sequences, etc. Keep in mind that appropriate thresholds are dependent on the application.
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Commonly, SAM files are processed in this order: 1.
- SAM files are converted into BAM files (samstools view)
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- BAM files are sorted by reference coordinates (samtools sort)
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- Sorted BAM files are indexed (samtools index)
Each step above can be done with commands below
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