Changes between Version 13 and Version 14 of SOPs/chip_seq_peaks


Ignore:
Timestamp:
03/25/15 16:31:38 (10 years ago)
Author:
ibarrasa
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • SOPs/chip_seq_peaks

    v13 v14  
    3434Based on our ChIP-Seq bake off and on a published review ([[http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011471|Evaluation of ChIP-Seq performance]]), MACs and SISSRs are good programs to try.
    3535
     36
     37==== MACS2 ====
     38
     39  * MACS2 is appropriate for both proteins like transcription factors that may have narrow peaks, as well as histone modifications that may affect broader regions. For broader peaks we recommend using --nomodel,--broad,  --nolambda (if there's no control), and using the fragment size calculated on the strand cross correlation analysis.  We recommend using macs2 rather than macs14 for broad peaks.  Identifying reproducible peaks (across replicates) with IDR requires MACS2 and works best with a relaxed p-value threshold.
     40{{{
     41bsub macs2 callpeak -t IP_reads.mapped_only.bam -c Control_reads.mapped_only.bam -f BAM -g mm -n Name --nomodel -B
     42bsub macs2 callpeak -t IP_reads.mapped_only.bam -c Control_reads.mapped_only.bam -f BAM -g mm -n Name -B -p 1e-3
     43}}}
     44  * --nomodel  whether or not to build the shifting model. If True, MACS will not build model. By default it means shifting size = 100.                     
     45  * -f Input format
     46  * -B create bedgraph output files
     47  * For future IDR analysis, use '-p 1e -3' => Set p-value cutoff to 1e-3 (which is more relaxed than the default setting)
     48
    3649==== MACS14 ====
     50We now recommend using macs2. Below is our previous recommendations on how to use macs1.4
    3751  * For MACS to work the header of the sequences can have no spaces.
    3852  * The command 'macs' points to macs14 on WIBR local machines
    … …  
    7791
    7892
    79 ==== MACS2 ====
    80 
    81   * MACS2 is appropriate for both proteins like transcription factors that may have narrow peaks, as well as histone modifications that may affect broader regions. For broader peaks we recommend using --nomodel,--broad,  --nolambda (if there's no control), and using the fragment size calculated on the strand cross correlation analysis.  We recommend using macs2 rather than macs14 for broad peaks.  Identifying reproducible peaks (across replicates) with IDR requires MACS2 and works best with a relaxed p-value threshold.
    82 {{{
    83 bsub macs2 callpeak -t IP_reads.mapped_only.bam -c Control_reads.mapped_only.bam -f BAM -g mm -n Name --nomodel -B
    84 bsub macs2 callpeak -t IP_reads.mapped_only.bam -c Control_reads.mapped_only.bam -f BAM -g mm -n Name -B -p 1e-3
    85 }}}
    86   * --nomodel  whether or not to build the shifting model. If True, MACS will not build model. By default it means shifting size = 100.                     
    87   * -f Input format
    88   * -B create bedgraph output files
    89   * For future IDR analysis, use '-p 1e -3' => Set p-value cutoff to 1e-3 (which is more relaxed than the default setting)
    90 
    9193==== SISSRs ====
    9294[[http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/|SiSSRs]] ([[http://nar.oxfordjournals.org/cgi/content/full/36/16/5221|Reference]]) ([[http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/SISSRs-Manual.pdf|Manual]])