BETA for RNA-Seq and ChIP-Seq Data Integration

Question

[benjyrolls]

Hello,

I have a Cuffdiff file output from RNA-Seq study and a bed file from MACS from my ChIP-Seq study. RNA-Seq study involved a Knockdown of p53 vs wild type mouse and chiPseq study involved wt vs p53 enriched chip.

I am using the public Cistrome server here

The default gene expression file from Cuffdiff does not have RefSeq IDs but Cufflinks IDs(XLOC ...) and the official gene symbol.

For some reason BETA is unable to accept the official gene symbol but wants its Ref seq ID instead before it can run.

1. Is there a way to convert Cuffdiffs Gene ID to Ref seq IDs using the gene expression file from Cuffdiff ?

2. Whats is the best tool to do integration of RNA-Seq and ChIP-Seq study ?

3. I have uploaded my expression RNA Seq graphs to UCSC genome browser along with my MACS treat pileup bedgraph, is there a way for me to make conclusions based on this approach for RNA-Seq and ChIP-Seq integration ? Thanks Ben

[James Ashmore]

If you use the command-line version you can pass the --gname2 flag and that will allow you to use just the gene symbol.

[benjyrolls]

Thanks for the reply. I found out I had to delete the header in the Cuffdiff output before the web one had to work. The --gname in the command line works as well.