correlating chipseq and rnaseq

[chipmonk]

I have done ChIPseq on a Bombyx TF protein. The genome of bombyx is not very well annotated. Therefore I also am doing some tissue specific RNAseq to supplement the chipseq list of peaks. I also think a denovo assembly of the transcriptome independent of the currently available genome would help find more cds regions which may not be yet sequenced. The primary purpose of rnaseq for me though is to determine the upregulated and downregulated regions in two tissues i compare and correlate to chipseq peaks.

I am not a bioinformatician by training but I have used tools like bowtie macs and samtools on linux. I wanted to know as to how to go about comparing chipseq peaks and the rnaseq data. what tools can be used. I have an additional issue of not having a good annotation or ucsc browser at my disposal however Ensembl has the genome and some data on bombyx.

Is there a way to build a GTF/GFF file from microarray probe list and EST sequences with homolog detail to make an annotation. again what tools to do these customization.

please do help