Structural Variations using RNA-Seq

[luciano.cascione]

Hello everybody,

I'm quite new in NGS. I'm looking for tools/stuff/idea to find Structural Variation (large deletion or tandem duplication) using RNA-Seq dataset (Illumina 100bp pair-end reads).

Could I use delly? This algorithm should work with DNA-Seq, may I use it with my RNA-Seq dataset?

So I look to the community if anyone can help me in my search for deletion.

Thank you for any help you can provide.

Luciano

[TiborNagy]

I think finding structural variation in RNA-seq is tricky, because very hard to differentiate isoforms and real structural variations. So I prefer paired-end DNA-Seq to find large deletions.

[shi]

Hello everybody,

I'm quite new in NGS. I'm looking for tools/stuff/idea to find Structural Variation (large deletion or tandem duplication) using RNA-Seq dataset (Illumina 100bp pair-end reads).

Could I use delly? This algorithm should work with DNA-Seq, may I use it with my RNA-Seq dataset?

So I look to the community if anyone can help me in my search for deletion.

Thank you for any help you can provide.

Luciano

You may try the subjunc aligner in Subread package. It can find up to 200bp indels in RNA-seq data.