detect DNA damage in NGS data

[ndeshpan]

Hi ,

We have conducted an RNASeq experiment (control vs bacterial infection 3 replicates : host) and identified a few DE genes in the host which hint towards possible DNA damage regulation in infected samples.

Can anyone with experience in the field tell us if it is possible to identify the extent of DNA damage in the actual host gene sequences by some how comparing the control reads to infection reads ?

Appreciate your assistance,

Nandan

[kokonech]

One possiblity is to search for gene fusions and other transcriptome rearrangements.
There are tools out there which are targted on this like for example deFuse, TophatFusion or ChimeraScan.

I'm also working on one, also in the context of DNA damage upon infection, you're welcome to try:

https://bitbucket.org/kokonech/infusion/wiki/Home

[ndeshpan]

Thanks kokonech..I will try out these tools..

Cheers,

Nandan