Hi,
I'm working on ChIP-seq and ChIP-chip TF datasets. My problem is caused by rGADEM and MotIV. I don't understand why sometimes, after GADEM(), my program return one matrix consensus and sometimes, it returns much matrix consensus...
My workflow use in first rGADEM to return fasta sequences and PWM. And in second, it uses MotIV to find TFBS on JASPAR database.
In the case where GADEM() return one matrix consensus, MotIV superposes enrichments motifs on the same plot and of course, i need calculate interdistance between 2 (and more) enrichments motifs.
I use the same script in the help. There are two things which changing : the input data and I modified database jaspar TFBS (in date 2010) in MotIV package to do corresponding to database plant jaspar TFBS (in date 2014).
I'm working on ChIP-seq and ChIP-chip TF datasets. My problem is caused by rGADEM and MotIV. I don't understand why sometimes, after GADEM(), my program return one matrix consensus and sometimes, it returns much matrix consensus...
My workflow use in first rGADEM to return fasta sequences and PWM. And in second, it uses MotIV to find TFBS on JASPAR database.
In the case where GADEM() return one matrix consensus, MotIV superposes enrichments motifs on the same plot and of course, i need calculate interdistance between 2 (and more) enrichments motifs.
I use the same script in the help. There are two things which changing : the input data and I modified database jaspar TFBS (in date 2010) in MotIV package to do corresponding to database plant jaspar TFBS (in date 2014).