search

comprna / SUPPA

SUPPA: Fast quantification of splicing and differential splicing
MIT License
244 stars 60 forks source link

U12 splicing event #180

Open jiehuichen opened 4 months ago

jiehuichen commented 4 months ago

Dear SUPPA team,

I'm very interested in U12 splicing events, I wonder if you will include U12 analysis in SUPPA?

By the way, based on your expertise, which algorithm can be used to analyze U12 splicing currently?

Thanks a lot.

Best, Jiehui

EduEyras commented 4 months ago

Hi Jiehui,

thanks for your interest in SUPPA

As SUPPA uses the annotations, U12 introns that are included in the annotation will also be used for the SUPPA analysis.

There are various approaches to identify U12 introns. Some are based on using directly ab-initio transcript predictions with evidence (e.g. Augustus) and others use a combination of comparisons to the U2 and U12 weight matrices for the 5' and 3' splice-sites.

For a recent search on U12 introns, see e.g. https://www.sciencedirect.com/science/article/pii/S0960982221005972

Once you have the annotations with U12 introns, all the alternative splicing analysis can be done as usual.

I hope this helps

E.

On Fri, 19 Jan 2024 at 12:47, Jiehui Chen @.***> wrote:

Dear SUPPA team,

I'm very interested in U12 splicing events, I wonder if you will include U12 analysis in SUPPA?

By the way, based on your expertise, which algorithm can be used to analyze U12 splicing currently?

Thanks a lot.

Best, Jiehui

— Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/180, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKBYCW55XBQOQW2DNCGDYPHGCZAVCNFSM6AAAAABCBGWEAOVHI2DSMVQWIX3LMV43ASLTON2WKOZSGA4DSMZZGY4TMMI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

jiehuichen commented 4 months ago

Hi Eduardo,

I appreciate your suggestions.

I found there are some U12 databases listed in Intron Annotation and Orthology Database (IAOD). https://introndb.lerner.ccf.org/sitepages/downloads/

About the analysis of U12 splicing in mice RNA-seq by SUPPA, is it reasonable to take the "GRCm38_U12.bed" file listed on the website as the annotation (may need to convert it to GTF format)?

https://introndb.lerner.ccf.org/static/bed/GRCm38_U12.bed

Thanks a lot.

Jiehui

EduEyras commented 4 months ago

Hi Jiehui,

SUPPA operates with a GTF file with the full annotation.

If you're only interested in the alternative splicing of U12 introns, you could first calculate all AS events, and then check which ones overlap with your U12 intron dataset.

Best

Eduardo

On Sat, 20 Jan 2024 at 02:04, Jiehui Chen @.***> wrote:

Hi Eduardo,

I appreciate your suggestions.

I found there are some U12 databases listed in Intron Annotation and Orthology Database (IAOD). https://introndb.lerner.ccf.org/sitepages/downloads/

About the analysis of U12 splicing in mice RNA-seq by SUPPA, is it reasonable to take the "GRCm38_U12.bed" file listed on the website as the annotation (may need to convert it to GTF format)?

https://introndb.lerner.ccf.org/static/bed/GRCm38_U12.bed

Thanks a lot.

Jiehui

— Reply to this email directly, view it on GitHub https://github.com/comprna/SUPPA/issues/180#issuecomment-1900587877, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADCZKBY7WT45QMZLCRBD7FLYPKDPTAVCNFSM6AAAAABCBGWEAOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBQGU4DOOBXG4 . You are receiving this because you commented.Message ID: @.***>

jiehuichen commented 4 months ago

Thanks a lot. It helps.

Best, Jiehui