which software or tool can be used for identifying alternative splicing events between control and dehydration library?

Question

[subhalakshmi.kandavel]

which software or tool can be used for identifying alternative splicing events between control and dehydration library?

Answer 1

[antonioggsousa]

Hi,

The 3D RNA-seq pipeline can be a good start.

Have a look into the paper: https://www.biorxiv.org/content/10.1101/656686v1

Have a look into the R package and code: https://github.com/wyguo/ThreeDRNAseq

Have a look into the Shiny app online (as web server): https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/

I hope this helps,

António

[antonioggsousa]

On top of what I said before, this paper comparing different tools for alternative splicing can be a good read too: https://academic.oup.com/bib/article/doi/10.1093/bib/bbz126/5648232

António

[subhalakshmi.kandavel]

Thank you Antonio.

So, I have 3 replicates for control, 6 hours and 12 hours stress(3 conditions) library RNA -seq data, i would like to do the 3 libraries all together in one go using some tool/ software ? , kindly anyone suggest for this purpose. Since i was using rMATS which can compare between only 2 conditions(like control & 6 hours at a time)i have to run rMATS in different combinations for 3 times.

[subhalakshmi.kandavel]

Thank you Antonio.

So, I have 3 replicates for control, 6 hours and 12 hours stress(3 conditions) library RNA -seq data, i would like to do the 3 libraries all together in one go using some tool/ software ? , kindly anyone suggest for this purpose. Since i was using rMATS which can compare between only 2 conditions(like control & 6 hours at a time)i have to run rMATS in different combinations for 3 times.

[antonioggsousa]

I never use rMATS. So, I'm not familiar.

Assuming that your 3 libraries represent a time-series experiment, where one stress/condition/treatment was tested across many times, the 3D RNA-seq might do what you want, since it has a tab to Time-series trend tab analysis (on the left side menu): https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/

António

[subhalakshmi.kandavel]

Thank you again. will try to do..