does peak in CHIP-seq mean the sequence depth in treatment sample will be bigger than control ?
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Entering edit mode
6.3 years ago
jimmy_zeng ▴ 90

For a region:

sequence depths in control ~~sample is like: 1,2,3,4,4,4,4,4,4,4,4,4,,4,4,4,,4,4,,4,4,4,3,3,2,1

sequence depths in treatment sample is like: 1,2,3,4,5,6,7,8,9,7,7,7,7,7,8,9,8,7,6,5,4,3,2,1,1

so this is the peak , yes or no ??

the depths in treatment must be higher than control !! and the depths in treatment should be double peaks ( if draws in figures) , and the depths in control must be a horizontal line , yes or right ?

The reason I have this question is

GSM1278641  Xu_MUT_rep1_BAF155_MUT  SRR1042593
GSM1278642  Xu_MUT_rep1_Input   SRR1042594
848M Jun 28 14:31 SRR1042593.bam
2.7G Jun 28 14:52 SRR1042594.bam
nohup time ~/.local/bin/macs2 callpeak -c SRR1042594.sam -t SRR1042593.sam -f SAM -p 0.01  -g hs -n Xu_MUT_rep1 2>Xu_MUT_rep1.masc2.log &    
samtools depth -r chr10:42385331-42385599 SRR1042593.sorted.bam
samtools depth -r chr10:42385331-42385599 SRR1042594.sorted.bam

both samples' depths have double peaks , and the depths in control are bigger than treatment !!! ???

which really confuse me .

sorry guys, I am really not familar with discribe the question in English, hope you can get it .

ChIP-Seq peaks MACS • 1.6k views
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Entering edit mode
6.3 years ago
SP ▴ 280

Your question is a little cryptic ;) but basis on what I can understand. Yes, if in treatment sample at certain region you have more enrichment of tags compared to control, that will qualify for a peak. But these are the problems which we leave on peak-callers (e.g. MACS, SICER, PeakRanger). You can do additional filtering on peaks based on their strength (e.g. a peak should minimum have 50 tags OR a peak with 500bp have atleast 50 tags). This will be a nice peak for me.

Treatment tag count:  3 4 5 5 5 7 8 12 15 24 25 30 25 18 13 13 8 5 5 4 3 3
Control tag count:    4 5 5 6 4 6 4 3 5 7 7 3 8 3 6 6 4 4 3 5 3 2 4 3 2 2 2

Example you have showed is not strong and could and could not be real peak. About depth: I would say the depth of sequencing should be similar in both samples (e.g +- 5 million). Even if depth in control is higher, a specifically bound region (peak) will be seen. Let me know if this helps.

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