fixed prokka ctg length

Author: HadrienG

16s.md

@@ -292,14 +292,23 @@ Otu0009	3618	Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100
 
 This is telling you that Otu0001 was observed 12328 times in your sample and that 100% of the sequences were from *Barnesiella*
 
-We'll visualize the composition of our datasets using Krona.
+<!-- We'll visualize the composition of our datasets using Krona.
 
 ```
 python mothur_krona_XML.py stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.an.unique_list.0.03.cons.tax.summary > mothur.xml
 ktImportXML mothur.xml
 ```
 
-Now open `xml.krona.html` in your browser!
+Now open `xml.krona.html` in your browser! -->
+
+In order to vizualise the composition of our datasets, we'll use phyloseq, a R package to work with microbiom data.
+
+Most of the phyloseq functionalities require aand a tree file. We need to generate it with mothur:
+
+```
+dist.seqs(fasta=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.fasta, output=lt, processors=8)
+clearcut(phylip=stability.trim.contigs.good.unique.good.filter.unique.precluster.pick.pick.phylip.dist)
+```
 
 
 ### Batch Mode
@@ -312,3 +321,22 @@ where script.batch (or whatever name you want, really) is a text file containing
 commands that you previously entered in interactive mode.
 
 If you have time, copy all the commands from this tutorial in a file, a try to make mothur work in batch mode!
+
+### 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:
+
+```R
+mothlist <- system.file("extdata", "esophagus.fn.list.gz", package="phyloseq")
+mothgroup <- system.file("extdata", "esophagus.good.groups.gz", package="phyloseq")
+mothtree <- system.file("extdata", "esophagus.tree.gz", package="phyloseq")
+
+show_mothur_cutoffs(mothlist)
+cutoff <- '0.10'
+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 

annotation.md

@@ -16,8 +16,9 @@ Alternatively, you can download an assembly [here](data/assembly.fasta)
 
 ```
 module load prokka
-prokka --compliant --centre SLU --outdir annotation \
-    --kingdom Bacteria --proteins m_genitalium.faa assembly.fasta
+awk '/^>/{print ">ctg" ++i; next}{print}' < assembly.fasta > good_contigs.fasta
+prokka --outdir annotation --kingdom Bacteria \
+--proteins m_genitalium.faa good_contigs.fasta
 ```
 
 Once Prokka has finished, examine each of its output files.