Entering edit mode
Hi,
I would like to use ChIPQC on rat ChIP-seq data that were generated using rn6 genome version. Despite another post explaining that it's possible to generate custom annotation (https://support.bioconductor.org/p/70893/), I haven't succeeded to do it myself for rn6.
Has anyone be able to do it?
Thanks, Fred
I don't think so. I guess the problem is that I don't know how to generate a ChIPQC custom annotation from
TxDb.Rnorvegicus.UCSC.rn6.refGene
.Could you tell me how to do that please?
Well it depends on what you want to use as your binding regions. If you want 'the usual' I guess there are two ways to go about it. You could 'cheat the system' (untested!) by doing
Which should then use the rn6
TxDb
package instead of the rn4 version. Or you could just make your own annotation, using the existinggetAnnotation
function.There may be a simpler, obvious way that I am missing, and perhaps Rory Stark or Tom Carroll will be along in a bit to clear that up. But I don't see a simple way to use a
TxDb
other than the choices they have hard-coded, so unfortunately it might take extra measures like this.Hi James,
Sorry I was away for a while.
But unfortunately the code is not working in my hands. Can you still help to find what is wrong?
Could
return(list(version=GeneAnnotation
be wrong here (you spoke about the existinggetAnnotation
yourself).I also got
Error in missing(AllChr) : 'missing' peut seulement être utilisé pour des arguments
eventually.Well, as you can see, I'm pretty lost here! Thanks!
Ah. My bad. Try
It works great. Thanks a lot for your help James!
Thank you for discussing this. I hope I can get help with my question. I found the above function useful for constructing a custom annotation file to proceed with ChIPQC package and downstream analysis. However, I couldn't understand why to provide semicolumn for rn6 in ChIPQC and custom function.
I am working on Rice genome (https://rapdb.dna.affrc.go.jp/). A custom txdb file is constructed using "makeTxDbFromGFF" function. We proceeded with the resultant txdb file to make an annotation file for ChIPQC package by following the script written above.
Here is the code for preparing the txdb.
Code given above
It ended up with the error displayed above.
Let me know if I am missing any basics in understanding the code.
Thank you