Changes between Version 19 and Version 20 of SOPs/chip_seq_peaks


Ignore:
Timestamp:
05/14/15 11:42:28 (10 years ago)
Author:
thiruvil
Comment:

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  • SOPs/chip_seq_peaks

    v19 v20  
    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. 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.
     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 (see [[http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#reporting | Bowtie2 Manual under Reporting ]]).
    1313
    1414 * See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping SOP]] for more details.