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Modifications to Mapping tutorial #57

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f9dc929
g-zipped versions of files not present. Corrected call accordingly
Sep 22, 2023
508b421
new invocation of mpileup as bcftools command ... instead of samtools
Sep 22, 2023
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7 changes: 3 additions & 4 deletions docs/mapping.md
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Expand Up @@ -41,8 +41,8 @@ bowtie2-build pO157_Sakai.fasta.gz pO157_Sakai
Now we are ready to map our reads

```bash
bowtie2 -x pO157_Sakai -1 SRR957824_trimmed_R1.fastq.gz \
-2 SRR957824_trimmed_R2.fastq.gz -S SRR957824.sam
bowtie2 -x pO157_Sakai -1 SRR957824_trimmed_R1.fastq \
-2 SRR957824_trimmed_R2.fastq -S SRR957824.sam
```

The output of the mapping will be in the SAM format.
Expand Down Expand Up @@ -95,8 +95,7 @@ For an EHEC O157 outbreak you could use it to identify the source, for instance.
We can call the variants using `samtools mpileup`

```bash
samtools mpileup -uD -f pO157_Sakai.fasta.gz SRR2584857.sorted.bam | \
bcftools view - > variants.vcf
bcftools mpileup -f pO157_Sakai.fasta.gz SRR2584857.sorted.bam
```

You can read about the structure of vcf files [here](file_formats.md).
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