Changes between Version 16 and Version 17 of SOPs/qc_shortReads

Timestamp:

09/15/14 17:28:12 (10 years ago)

Author:

thiruvil

Comment:

--

SOPs/qc_shortReads

@@ -184 +184 @@
     * much more conservative than fastx_clipper.
     * [wiki:SOPs/cutadapt sample usage]
+    * a vs b options from [[http://journal.embnet.org/index.php/embnetjournal/article/view/200|EMBnet.journal]]
+       [[Image(cutadapt.2.jpeg,500px)]]
     * sample command:
 
-{{{
-bsub cutadapt -a GATCGGAAGAGCTCGTATGCCGTCTT –o Nanog_noAdapter.fastq Nanog.fastq
-
-In the above command:
-   -a: Sequence of an adapter that was ligated to the 3' end.
-   -o:  output file name
-}}}
+    {{{
+    bsub cutadapt -a GATCGGAAGAGCTCGTATGCCGTCTT –o Nanog_noAdapter.fastq Nanog.fastq
+
+    In the above command:
+       -a: Sequence of an adapter that was ligated to the 3' end.
+       -o:  output file name
+    }}}
+
 
   * See [[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_clipper_usage|fastx_clipper usage]] (or ''fastx_clipper -h'') for more arguments