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dellytools / delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
BSD 3-Clause "New" or "Revised" License
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Inquiry on Using Delly for Identifying Transgene Insertion Sites in Mouse Genome #378

Open Zeyu618 opened 2 months ago

Zeyu618 commented 2 months ago

Dear Tobias,

I hope this message finds you well. 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 1400 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. Given the reputation of the delly software, which you developed, for its robust detection of structural variations, I am keen to understand its applicability to our specific research needs.

Could you please advise whether delly is suitable for identifying the locations of a known transgene within a complex genome such as that of the mouse? If delly 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 delly for this purpose, your insights would be invaluable.

Thank you very much for your time and assistance. I look forward to your expert advice and hopefully integrating delly into our workflow.

Warm regards,

Zeyu Chen

tobiasrausch commented 2 months ago

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.

Zeyu618 commented 2 months ago

Thank you for your swift response. To confirm, are we understanding correctly that the process involves merging the additional fasta sequence into the mouse genome, followed by analyzing inter-chromosome variations using DNA re-sequencing data? If so, we're happy to let you know that our ongoing approach aligns with your recommendations. Thank you again.