Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome

Question

[zec018]

I am currently engaged in a project that involves tracking the insertion sites of a transgene in the mouse genome. The transgene in question is approximately 1500 base pairs in length and has been randomly integrated into the mouse genome.

We have generated paired-end sequencing data (PE150) and are exploring the best methodologies to accurately pinpoint the insertion sites of this transgene.

Whether Delly/Pindel/breakdancer is suitable for identifying the locations of such known transgene within a complex genome such as that of the mouse? If any of them is applicable, I would appreciate any guidance or suggestions on how best to utilize the software for our particular scenario. Additionally, if there are any specific parameters or considerations we should be aware of when configuring for this purpose?

I would appreciate it if you give me some advice.

Thanks in advace.

Answer 1

[trausch]

For delly, we usually augment the mouse reference genome with the additional sequence, then remap and then look in the delly output for BND events linking the additional sequence to the regular mouse genome.