Changes between Version 18 and Version 19 of SOPs/chip_seq_peaks


Ignore:
Timestamp:
05/14/15 10:59:47 (10 years ago)
Author:
thiruvil
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/chip_seq_peaks

    v18 v19  
    1010=== Step 1: Map reads ===
    1111
    12  * Use [[http://bowtie-bio.sourceforge.net/tutorial.shtml|Bowtie]], [[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml|bowtie2]], or another unspliced mapping tool[[br]]
     12 * 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 q2 or higher) is not needed as Bowtie2 randomly chooses a best hit when multiple good hits exist.
    1313
    1414 * See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping SOP]] for more details.