Changes between Version 40 and Version 41 of SOPs/chip_seq_peaks


Ignore:
Timestamp:
08/09/17 15:31:35 (7 years ago)
Author:
thiruvil
Comment:

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  • SOPs/chip_seq_peaks

    v40 v41  
    1616=== Step 1: Map reads ===
    1717
    18  * 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] ]).
     18 * 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] ]).  Low mapping quality reads may need to be removed if using another aligner since MACS does not filter on mapping quality.
    1919
    2020 * See the [[http://barcwiki.wi.mit.edu/wiki/SOPs/mapping|mapping SOP]] for more details.