Changes between Version 34 and Version 35 of SOPs/qc_shortReads

Timestamp:

04/26/17 10:54:44 (8 years ago)

Author:

gbell

Comment:

--

SOPs/qc_shortReads

@@ -12 +12 @@
 == Naming ==
 
-FASTQ header/naming scheme as specified by, \\
+FASTQ header/naming scheme as specified by \\
+
 [[http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_FASTQFiles.htm | Illumina (Casava 1.8.2):]]\\
 @<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos> <read>:<is filtered>:<control number>:<index sequence>
@@ -30 +31 @@
 ||<index sequence>||ACTG||Index sequence||
 \\
-
 Illumina (Casava 1.7)\\
 @<machine_id>:<lane>:<tile>:<x_coord>:<y_coord>#<index>/<read_#>
@@ -60 +60 @@
 [[Image(fastq_phread-base.png)]]
 
-  from [[https://en.wikipedia.org/wiki/FASTQ_format | Wiki FASTQ Format]]
+  from [[https://en.wikipedia.org/wiki/FASTQ_format | Wikipedia's FASTQ page]]
 
 == FastQC ==
 
-http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc
+http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
   * quality control analysis with nice graphical output 
   * available for Linux, Windows, and MacOSX
@@ -192 +192 @@
 
 
-  * [[http://code.google.com/p/cutadapt/|cutadapt]] is a good tool that is designed to find and remove adapters:
+  * [[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.
@@ -264 +264 @@
 == Galaxy ==
 
-http://main.g2.bx.psu.edu/
+https://usegalaxy.org/
 Many functions \\