Transgene insertion using ChIP-seq data

Question

[sergio.espeso-gil]

Hi community,

I have ChIP-seq data from different histone marks and I think I can get the insertion sites of a trangene by clipping out the sequences from the extremes of the transgene. I have been trying to do it by mapping the transgene promoter using bowtie and trying to get the sequences, but it didn't work out. I did 50bp sequencing single strand.

Any ideas?

Thanks,
Sergio

Answer 1

[Devon Ryan]

You'll need to do microassembly (e.g., with mapsembler) using the transgene sequence. The biggest problem with this will be if your ChIP signal is very sharp or not near a transgene edge then you won't get enough coverage to find the insertion site(s). Just google around for microassemblers. You will also have problems if you have too many insertion sites (e.g., you're sequencing a highly diverse population), but there's no way around these issues given the data you apparently have.

[sergio.espeso-gil]

Thanks! That is a good start with. I will try.