Replicates in Chip-Seq

feralBiologist · 09-09-2013, 07:08 AM

I have the following dataset:

wild type:

2 male biol ChIP replicates for TF A
2 female biol ChIP replicates for TF B
1 male ChIP sample for TF C
1 male ChIP sample for TF D
1 male input sample (from one of the animals used for one of the samples for TF A)
1 female input sample (from one of the animals used for one of the samples for TF A)
knockouts:

1 male ChIP sample for TF A
1 pooled (male+female) ChIP sample for TF B
All animals are of similar age.

The main interest is the contrast between knockouts and wild types for TF A and TF B. I have the following questions:

(1) Does it make sense to take into account the samples for TF C and TF D?

(2) Does it make sense to take into account the sex (no sex-specific is effect is specifically expected)?

(3) How to make the best possible use of this data and which tool would you recommend? I have used macs. I am also aware about DiffBind, MEDIPS, diffreps and DBChIP but haven't used any of them so any specific recommendation regarding a tool and a workflow (if more than one tool is to be used) is most welcome.

ps. I cross-posted this on biostars: http://www.biostars.org/p/80829/

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09-09-2013, 07:08 AM	#1
feralBiologist Member Location: UK Join Date: Jun 2011 Posts: 61	Replicates in Chip-Seq I have the following dataset: wild type: 2 male biol ChIP replicates for TF A 2 female biol ChIP replicates for TF B 1 male ChIP sample for TF C 1 male ChIP sample for TF D 1 male input sample (from one of the animals used for one of the samples for TF A) 1 female input sample (from one of the animals used for one of the samples for TF A) knockouts: 1 male ChIP sample for TF A 1 pooled (male+female) ChIP sample for TF B All animals are of similar age. The main interest is the contrast between knockouts and wild types for TF A and TF B. I have the following questions: (1) Does it make sense to take into account the samples for TF C and TF D? (2) Does it make sense to take into account the sex (no sex-specific is effect is specifically expected)? (3) How to make the best possible use of this data and which tool would you recommend? I have used macs. I am also aware about DiffBind, MEDIPS, diffreps and DBChIP but haven't used any of them so any specific recommendation regarding a tool and a workflow (if more than one tool is to be used) is most welcome. ps. I cross-posted this on biostars: http://www.biostars.org/p/80829/