Update required on "Inspection of a BAM file" section.

[mthang]

training-material/topics/sequence-analysis/tutorials/mapping/tutorial.md

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# Inspection of a BAM file

Some discrepancies found when delivering a workshop using Mapping Tutorial.

1. Samtools stats (2.0.2+galaxy2).

   • Use a reference sequence : Locally cached/Use a built-in genome (on the GTN) vs Locally cached ( correct version )
   • Using genome : Mouse (Mus musculus): mm10 Full (on the GTN) vs Mouse (Mus musculus): mm10 ( correct version)

2. The output of the samtools stats before filtering

   • The samtools output is not consistent with what's on the GTN.
   • ~21,900 mismatches (on the GTN) vs 32663 ( actual output in the report)
   • ~4,753,900 bases mapped (on the GTN) vs 5004018 ( actual output in the report)
   • ~0.005 mismatches per mapped base (on the GTN) vs 6.527354e-03 ( actual output in the report)

3. The output of the samtools stats after filtering

   • Before filtering: 95,412 reads and after filtering: 89,664 reads. (on the GTN)
   • Reads mapped : 92152 and read properly paired 90644 ( actual output in the report) ??