User:Karmella Haynes/Notebook/PcTF Genomics/2012/05/16: Difference between revisions

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* Arguments and parameters in Excel files from Mark
* Arguments and parameters in Excel files from Mark
** About this run: Attempted to use a no-antibody mock IP (sample 6) as baseline/ noise for the real IP of H3K27me3 (sample 1)
** About this run: Attempted to use a no-antibody mock IP (6_aln.bam) as baseline/ noise for the real IP of H3K27me3 (1_aln.bam)


{| class="wikitable" border="0" cellspacing="3" <!-- Rxn. table -->
{| class="wikitable" border="0" cellspacing="3" <!-- Rxn. table -->
Line 25: Line 25:
| <u>Parameter</u> || <u>Sample 1</u> || <u>Sample 6</u>
| <u>Parameter</u> || <u>Sample 1</u> || <u>Sample 6</u>
|-
|-
| name || NA
| name || NA || NA
|-
|-
| format || AUTO
| format || AUTO || AUTO
|-
|-
| ChIP-seq file || /scratch/mwteng/haynes/aligned/bam/1_aln.bam
| ChIP-seq file || /scratch/mwteng/haynes/aligned/bam/1_aln.bam || /scratch/mwteng/haynes/aligned/bam/6_aln.bam
|-
|-
| Control file || None
| Control file || None || None
|-
|-
| Effective genome size || 2.7e+09
| Effective genome size || 2.7e+09 || 2.7e+09
|-
|-
| Band width || 300
| Band width || 300 || 300
|-
|-
| Model fold || 10,30
| Model fold || 10,30 || 10,30
|-
|-
| P value cut-off || 1.00e-05
| P value cut-off || 1.00e-05 || 1.00e-05
|-
|-
| Tag size determined as || 100 bps
| Range for calc. regional lamba || || 10,000 bps
|-
|-
| Total tags || 8,207,576
| Tag size determined as || 100 bps || 100 bps
|-
|-
| Tags after filtering || 1,076,608
| Total tags || 8,207,576 || 106,569,524
|-
|-
| Maximum duplicate tags || 1
| Tags after filtering || 1,076,608 || 4,947,906
|-
|-
| Redundant rate || 0.87
| Maximum duplicate tags || 1 || 1
|-
| Redundant rate || 0.87 || 0.95
|-
| d || || 233
|}
|}


Revision as of 17:38, 2 April 2014

Pc-TF Genomics <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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05/16/12

  • Peak-finding: BAM > BED using MACS


Peak-finding: BAM > BED using MACS

  • Done by Mark Teng
  • 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
    • About this run: Attempted to use a no-antibody mock IP (6_aln.bam) as baseline/ noise for the real IP of H3K27me3 (1_aln.bam)
Parameter Sample 1 Sample 6
name NA NA
format AUTO AUTO
ChIP-seq file /scratch/mwteng/haynes/aligned/bam/1_aln.bam /scratch/mwteng/haynes/aligned/bam/6_aln.bam
Control file None None
Effective genome size 2.7e+09 2.7e+09
Band width 300 300
Model fold 10,30 10,30
P value cut-off 1.00e-05 1.00e-05
Range for calc. regional lamba 10,000 bps
Tag size determined as 100 bps 100 bps
Total tags 8,207,576 106,569,524
Tags after filtering 1,076,608 4,947,906
Maximum duplicate tags 1 1
Redundant rate 0.87 0.95
d 233




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