User:Karmella Haynes/Notebook/PcTF Genomics/2012/05/16: Difference between revisions
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* MACS: Model-based Analysis of ChIP-Seq (Zhang et al. 2008) - Given a sonication size (bandwidth) and a high-confidence fold-enrichment (mfold), MACS slides 2 bandwidth windows across the genome to find regions with tags more than mfold enriched relative to a random tag genome distribution. | * MACS: Model-based Analysis of ChIP-Seq (Zhang et al. 2008) - Given a sonication size (bandwidth) and a high-confidence fold-enrichment (mfold), MACS slides 2 bandwidth windows across the genome to find regions with tags more than mfold enriched relative to a random tag genome distribution. | ||
* | * Arguments and parameters in Excel files from Mark | ||
{| class="wikitable" border="0" cellspacing="3" <!-- Rxn. table --> | {| class="wikitable" border="0" cellspacing="3" <!-- Rxn. table --> | ||
|-valign="top" | |-valign="top" | ||
| <u>Parameter</u> || <u> | | <u>Parameter</u> || <u>Value</u> | ||
|- | |- | ||
| | | name || NA | ||
|- | |- | ||
| | | format || AUTO | ||
|- | |- | ||
| | | ChIP-seq file || /scratch/mwteng/haynes/aligned/bam/1_aln.bam | ||
|- | |- | ||
| | | Control file || None | ||
|- | |- | ||
| | | Effective genome size || 2.7e+09 | ||
|- | |- | ||
| Band width || 300 | |||
|- | |||
| Model fold || 10,30 | |||
|- | |||
| P value cut-off || 1.00e-05 | |||
|- | |||
| | |||
| || # μL | | || # μL | ||
|} | |} | ||
Revision as of 14:09, 2 April 2014
 Pc-TF Genomics
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05/16/12
Peak-finding: BAM > BED using MACS
--> Reaction conditions
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