sam to bam

Author: HadrienG

16s.md

@@ -324,9 +324,7 @@ If you have time, copy all the commands from this tutorial in a file, a try to m
 
 ### PhyloSeq Analysis
 
-The PhyloSeq package has an `import_mothur` function that you can use to import the files you generated with mothur.
-
-To simplify the tutorial, we will use the example data provided with the phyloseq package:
+The PhyloSeq package has an `import_mothur` function that you can use to import the files you generated with mothur. As an example, import the example mothur data provided by phyloseq as an example:
 
 ```R
 mothlist <- system.file("extdata", "esophagus.fn.list.gz", package="phyloseq")
@@ -339,4 +337,16 @@ x <- import_mothur(mothlist, mothgroup, mothtree, cutoff)
 x
 ```
 
-Note: If if you ever work with 16s data and decide to use QIIME instead of mothur, phyloseq also has an `import_qiime` function. Also, newer version of qiime and mothur have the ability to produce a `.biom` file 
+Note: If if you ever work with 16s data and decide to use QIIME instead of mothur, phyloseq also has an `import_qiime` function. Also, newer version of qiime and mothur have the ability to produce a `.biom` file.
+
+> “The biom file format (canonically pronounced ‘biome’) is designed to be a general-use format for representing counts of observations in one or more biological samples. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium candidate project.”
+
+More info on [http://biom-format.org/](http://biom-format.org/)
+
+For the rest of this tutorial, we will work with an example dataset provided by the phyloseq package. Load the data with the following command:
+
+
+```R
+data(enterotype)
+enterotype
+```

variant_calling.md

@@ -77,7 +77,7 @@ First you need to sort the reads in the BAM-file so the variant caller can easil
 
 You may need to convert your sam file into a bam file first:
 
-`samtools view -b -o $output.bam $input.sam`
+`samtools view -bS -o $output.bam $input.sam`
 
 then sort and index the bam file: