Question: which software or tool can be used for identifying alternative splicing events between control and dehydration library?
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gravatar for subhalakshmi.kandavel
27 days ago by
subhalakshmi.kandavel0 wrote:

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

rna-seq • 135 views
ADD COMMENTlink modified 27 days ago by antonioggsousa910 • written 27 days ago by subhalakshmi.kandavel0
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gravatar for antonioggsousa
27 days ago by
antonioggsousa910 wrote:

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

ADD COMMENTlink written 27 days ago by antonioggsousa910

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

ADD REPLYlink written 27 days ago by antonioggsousa910

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.

ADD REPLYlink written 15 days ago by subhalakshmi.kandavel0

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.

ADD REPLYlink written 15 days ago by subhalakshmi.kandavel0

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

ADD REPLYlink written 15 days ago by antonioggsousa910

Thank you again. will try to do..

ADD REPLYlink written 13 days ago by subhalakshmi.kandavel0
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