|
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 analyze IP of hPc-TF (1_aln.bam) and H3K27me3 (6_aln.bam)
- 04-03/14 Note: no ChIP input sequencing sample was used; I did the input HiSeq experiment later in 2013
| 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 lambda |
10,000 bps |
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 |
104 |
233
|
|
Pc-TF Genomics
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