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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/
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/