Please go to http://sourceforge.net/projects/seqminer/ to download the last version of seqMINER.
We have added a third beta test panel named Advanced(RNA-seq). This function helps us to do the comparison between Chipseq and Rnaseq datasets.
A genome assembly must be selected before the further analysis. Recent human and mouse assembly are already provided in the combo box. You can also try to extract the assembly information with Ensembl — biomart (http://www.ensembl.org/biomart/martview/). After selecting the database, you should select the attributes in this order:
Gene Start (bp)
Gene End (bp)
Ensembl Gene ID
Associated Gene Name
Finally you can export the result in text format to the 'lib' under the seqminer folder.(just the same format as the other .seqminer files)
To do the clustering, we should unfortunately go to the first panel(Density Array Method), the KMeans enrichment and KMeans enrichement linear normalization methods which give one enrichment value to a peak region should be more suitable to this kind of analysis.
Meanwhile, the chipseq peak annotation is available as a benefit of the RNAseq module. At this moment, only the gene the most close to a peak will be annotated.(a selection of genome assambly is however required)