added some alignment diagnostics

vsbuffalo · Jun 29, 2012 · d72acda · d72acda
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diff --git a/README.md b/README.md
@@ -81,3 +81,14 @@ script to allow this to be parallelizable.
 
 I am using `-N1` with `gsnap`, which allows for novel
 splicing. `gsnap` also allows for known splicing junctions to be used.
+
+## Converting SAM files to BAM files
+
+Another task for `xargs`. As before, I use basename to keep just the
+unique file name as a key, and run `samtools` with the correct
+directory and extension. This allows me to change the extension too.
+
+    find data/alignments/ -name "*sam" | xargs -n1 -I{} basename {} .sam | xargs -n1 -I{} -P4 samtools view -b -S -o data/alignments/{}.bam data/alignments/{}.sam
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+
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diff --git a/raw-read-qa.Rmd b/raw-read-qa.Rmd
@@ -1,4 +1,4 @@
-# Raw Read Quality Assessment
+# Raw and Processed Read Quality Assessment
 
 It's extremely important to do quality assessment and improvement
 steps before working with sequencing data. I highly recommend this one