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added some alignment diagnostics

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commit d72acdab4b3049f12a86c05c556a047302a5687e 1 parent eb23f7a
@vsbuffalo authored
Showing with 12 additions and 1 deletion.
  1. +11 −0
  2. +1 −1  raw-read-qa.Rmd
@@ -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
2  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

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