Changes between Version 40 and Version 41 of SOPs/qc_shortReads

Timestamp:

08/30/17 10:42:44 (7 years ago)

Author:

gbell

Comment:

--

SOPs/qc_shortReads

@@ -207 +207 @@
 
 
-  * [[https://cutadapt.readthedocs.io/en/stable/|cutadapt]] is a good tool that is designed to find and remove adapters:
+  * '''Method 1''': [[https://cutadapt.readthedocs.io/en/stable/|cutadapt]] is a good tool that is designed to find and remove adapters:
     * more options than fastx_clipper, such as specifically trimming 5' or 3' adapters and specifying error rate (allowed mismatches)
     * much more conservative than fastx_clipper.
@@ -213 +213 @@
     * a vs b options from [[http://journal.embnet.org/index.php/embnetjournal/article/view/200|EMBnet.journal]]
        [[Image(cutadapt.2.jpeg,500px)]]
-    * sample command:
-
+       * sample command:
     {{{
     bsub cutadapt -a GATCGGAAGAGCTCGTATGCCGTCTT -o Nanog_noAdapter.fastq Nanog.fastq
@@ -224 +223 @@
 
 
-  * See [[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_clipper_usage|fastx_clipper usage]] (or ''fastx_clipper -h'') for more arguments
-  * sample command:
-
+  * '''Method 2''': [[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_clipper_usage|fastx_clipper]]
+    * Sample command:
 {{{
 bsub "fastx_clipper -a CTGTAGGCACCATCAAT -i s2_sequence.txt -v -l 22 -o s2_sequence_noLinker.txt"  # fastq input and output
@@ -240 +238 @@
 }}}
 
-
-  * If you get the message "Invalid quality score value..." you have the older range of quality scores.
-    * Add the argument -Q 33, such as
-    * fastx_clipper -a CTGTAGGCACCATCAAT -Q 33 -i s2_sequence.txt -v -l 22 -o s2_sequence_noLinker.txt
+      * See [[http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_clipper_usage|fastx_clipper usage]] (or ''fastx_clipper -h'') for more arguments
+      * If you get the message "Invalid quality score value..." you have the older range of quality scores.
+        * Add the argument -Q 33, such as
+        * fastx_clipper -a CTGTAGGCACCATCAAT -Q 33 -i s2_sequence.txt -v -l 22 -o s2_sequence_noLinker.txt
+
+  * '''Method 3''': [[https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/|Trim Galore!]] combines cutadapt, FastQC, and the ability to guess what your adapters are 
+     * Sample command
+{{{
+# Usage : trim_galore [options] <filename(s)>
+trim_galore --phred64 --fastqc  -o my_trimmed_reads raw_reads/My_reads.fq.gz
+# Get all options
+trim_galore --help
+
+--phred64 ==> Use Illumina 1.5 encoding quality scores
+--fastqc ==> Run FastQC after trimming
+-o ==> Print output files in this directory instead of the current directory
+}}}
 
 == Trim reads to a specified length ==
    * If we have reads of different lengths (//i.e.// because we clipped out the adapter sequences), we can trim them to have them all be the same length. Use **fastx_trimmer** for that.
    * sample command: 
-
- 
 {{{
 bsub "fastx_trimmer -f 1 -l 22  -i s7_sequence_clipped.txt -o s7_sequence_clipped_trimmed.txt"  # fastq input and output