Changes between Version 35 and Version 36 of SOPs/qc_shortReads

Timestamp:

04/26/17 12:00:03 (8 years ago)

Author:

thiruvil

Comment:

--

SOPs/qc_shortReads

@@ -64 +64 @@
 == FastQC ==
 
-http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
+[[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/|FastQC]]
   * quality control analysis with nice graphical output 
   * available for Linux, Windows, and MacOSX
@@ -88 +88 @@
 
 == ShortRead (R package) ==
-http://www.bioconductor.org/packages/release/bioc/html/ShortRead.html
+[[http://www.bioconductor.org/packages/release/bioc/html/ShortRead.html| ShortRead]]
 R package, Linux (Tak), Window, Mac \\
 
@@ -114 +114 @@
 
 == Fastx Toolkit ==
-http://hannonlab.cshl.edu/fastx_toolkit/
+[[http://hannonlab.cshl.edu/fastx_toolkit/|FastX Toolkit]]
 galaxy integration, Linux(Tak), MacOSX \\
 '''Note:''' fastq_quality_filter v 0.0.14 may have a bug where it reports "got empty array at fastq_quality_filter.c:97" and/or segmentation fault.
@@ -131 +131 @@
 
 \\
+ 
+== PrinSeq ==
+[[http://prinseq.sourceforge.net | PrinSeq]] gives summary statistics and QC, eg. remove duplicate reads (eg. exact duplicate and other options) and has several visual summaryies.
+
+{{{
+#Get html summary of output
+prinseq-lite.pl -fastq myFile.fastq -graph_data file.gd -out_good null -out_bad null
+prinseq-graphs.pl -i file.gd -html_all -o prinseq_outFile
+
+#remove exact duplicates (drep=1) to a new fastq file
+prinseq-lite.pl -fastq myFile.fastq -derep 1 -out_good myFile.unique.fq -out_bad myFile.dup.fastq
+
+}}}
 
 = Modifying a file of short reads based on quality considerations =