Input data sets for IM-fusion

[xflicsu]

I have three questions for using IM-fusion:

1. Your article identify TE insertions from RNA-Seq based on Sleeping Beauty (SB) transposon model. But, I have several RNA-Seq data sets from Normal vs Tumor paired samples. Are my data sets suitable for insertion detection by using IM-fusion?
2. I wonder any other transposon elements are suitable for IM-fusion?
3. And how can I prepare for these files?

Best,

[jrderuiter]

Hi @xflicsu,

If your files contain transposon insertions from an insertional mutagenesis screen, you should be able to analyse them with IM-Fusion. Note that you need to supply two files for IM-Fusion to be able to recognise your insertion:

• A sequence file containing the transposon sequence.
• A feature file (CSV) describing the positions of splice-donor and splice-acceptor sequences in your transposon sequence.

Example files for the PB and SB transposons are given here: https://github.com/NKI-CCB/imfusion/tree/develop/data

Best, Julian