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Casey Dunn committed 72e2530

removed pdf stuff

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 # An SRA summary tool
 
-To execute the analysis, run:
+To execute the analysis in R, run:
+
+    library(knitr)
+    knit2html("sra_summary.rmd")
+
+This produces output files in two different formats, `sra_summary.rm` and 
+`sra_summary.html`.
 
-    ./knit sra_summary.rmd
-    
 See `sra_summary.rmd` for more details.

knit

-#!/bin/bash
-
-FULLFILE=$1
-
-#FILENAME=$(basename "$FULLFILE")
-#extension="${filename##*.}"
-FILENAME="${FULLFILE%.*}"
-
-echo $FILENAME
-
-Rscript -e "require(knitr); require(markdown); knit('$FULLFILE', '$FILENAME.md')"
-
-pandoc $FILENAME.md -o $FILENAME.pdf
-
-open $FILENAME.pdf
-
-
-
 <body>
 <h1>Metazoan SRA summary</h1>
 
+<p>Last updated Sat Jan 18 08:36:51 2014.</p>
+
 <h2>Getting the SRA data</h2>
 
 <p>Go to <a href="http://www.ncbi.nlm.nih.gov/sra">http://www.ncbi.nlm.nih.gov/sra</a> , and make the following query:</p>
 
-<p>&ldquo; (&quot;strategy rna seq&rdquo;[Properties] OR transcriptomic[Text Word]  OR cDNA[Text Word] ) AND &ldquo;platform illumina&rdquo;[Properties] AND metazoa[Organism] NOT vertebrata[Organism] NOT insects[Organism]) AND (&ldquo;2000/01/01&rdquo;[Modification Date] : &ldquo;3000&rdquo;[Modification Date]</p>
+<pre><code>(&quot;strategy rna seq&quot;[Properties] OR transcriptomic[Text Word]  OR cDNA[Text Word] ) AND &quot;platform illumina&quot;[Properties] AND metazoa[Organism] NOT vertebrata[Organism] NOT insects[Organism]) AND (&quot;2000/01/01&quot;[Modification Date] : &quot;3000&quot;[Modification Date]
+</code></pre>
 
-<pre><code>
-Then click &quot;Send To&quot; and select &quot;File&quot; and &quot;Summary&quot;. This will download the file `sra_result.csv`.
+<p>Then click &ldquo;Send To&rdquo; and select &ldquo;File&rdquo; and &ldquo;Summary&rdquo;. This will download the file <code>sra_result.csv</code>.</p>
 
-Then load the data:
+<p>Then load the data:</p>
 
-```r
-D &lt;- read.csv(&quot;sra_result.csv&quot;)
+<pre><code class="r">D &lt;- read.csv(&quot;sra_result.csv&quot;)
 </code></pre>
 
 <p>This gives a total of 2296 samples.</p>
 # Metazoan SRA summary
 
+Last updated Sat Jan 18 08:36:51 2014.
+
 ## Getting the SRA data
 
 Go to http://www.ncbi.nlm.nih.gov/sra , and make the following query:
 
-``` ("strategy rna seq"[Properties] OR transcriptomic[Text Word]  OR cDNA[Text Word] ) AND "platform illumina"[Properties] AND metazoa[Organism] NOT vertebrata[Organism] NOT insects[Organism]) AND ("2000/01/01"[Modification Date] : "3000"[Modification Date]
-```
+    ("strategy rna seq"[Properties] OR transcriptomic[Text Word]  OR cDNA[Text Word] ) AND "platform illumina"[Properties] AND metazoa[Organism] NOT vertebrata[Organism] NOT insects[Organism]) AND ("2000/01/01"[Modification Date] : "3000"[Modification Date]
+
 
 Then click "Send To" and select "File" and "Summary". This will download the file `sra_result.csv`.
 

sra_summary.pdf

Binary file removed.
 # Metazoan SRA summary
 
+Last updated `r date()`.
+
 ## Getting the SRA data
 
 Go to http://www.ncbi.nlm.nih.gov/sra , and make the following query:
 
-``` ("strategy rna seq"[Properties] OR transcriptomic[Text Word]  OR cDNA[Text Word] ) AND "platform illumina"[Properties] AND metazoa[Organism] NOT vertebrata[Organism] NOT insects[Organism]) AND ("2000/01/01"[Modification Date] : "3000"[Modification Date]
-```
+    ("strategy rna seq"[Properties] OR transcriptomic[Text Word]  OR cDNA[Text Word] ) AND "platform illumina"[Properties] AND metazoa[Organism] NOT vertebrata[Organism] NOT insects[Organism]) AND ("2000/01/01"[Modification Date] : "3000"[Modification Date]
+
 
 Then click "Send To" and select "File" and "Summary". This will download the file `sra_result.csv`.