Changes between Version 39 and Version 40 of SOPs/chip_seq_peaks

Timestamp:

04/27/17 08:10:23 (8 years ago)

Author:

gbell

Comment:

--

SOPs/chip_seq_peaks

@@ -16 +16 @@
 === Step 1: Map reads ===
 
- * Use [[http://bowtie-bio.sourceforge.net/tutorial.shtml|Bowtie]], [[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml|bowtie2]], or another unspliced mapping tool. We recommend using Bowtie2 (default parameters), filtering to remove multi-mapped reads (eg. a mapping quality of 2 or higher) is not needed as Bowtie2 randomly chooses a best hit when multiple good hits exist (see [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#reporting | Bowtie2 Manual under Reporting ]]).
+ * Use [[http://bowtie-bio.sourceforge.net/tutorial.shtml|Bowtie]], [[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml|bowtie2]], or another unspliced mapping tool. We recommend using Bowtie2 (default parameters), filtering to remove multi-mapped reads (eg. a mapping quality of 2 or higher) is not needed as Bowtie2 randomly chooses a best hit when multiple good hits exist (see [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#reporting | Bowtie2 manual [under Reporting] ]).
 
  * See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping SOP]] for more details.
@@ -112 +112 @@
 
 ==== SISSRs ====
-[http://sissrs.rajajothi.com/ SiSSRs] ([https://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/SISSRs-Manual.pdf Manual]) 
+[http://sissrs.rajajothi.com/ SiSSRs] ([https://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/SISSRs-Manual.pdf manual]) 
 [[chipSeqBakeOff|ChIP-Seq bake off]]
 
@@ -144 +144 @@
   * -m is the percentage of mappable bps. Default is .8 for Eland in human.
 
-For more detailed description of parameters see [[chipSeqBakeOff|ChIP-Seq bake off]]
+For more detailed description of parameters see our [chipSeqBakeOff ChIP-Seq bake off].