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wososa / PSI-Sigma

PSI-Sigma
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motif discovery #49

Closed parsboy66 closed 1 year ago

parsboy66 commented 1 year ago

Dear woody,

is there any scripts to extract the fasta from the specific events and prepare it for motif discovery?? or any suggestions, ways to do it ?

Thanks iman

wososa commented 1 year ago

Dear @parsboy66 ,

you will find how to extract sequences in Day 2 workshop.

Best, Woody

wososa commented 1 year ago

Hi @parsboy66 ,

Is this issue resolved?

Thanks, Woody

parsboy66 commented 1 year ago

Dear Woody, yes, actually I use Genome alignment to extract the region of interest (in my case exon skipping parts) and create that fastA file used in MEMEsuit to find the motifs. now I have another issue: exon skipping at the output of the PSI-sigma shows the PSI of the exon which skipped, while the PSI is the percent splice in. I'm now confused between these terms. could you please elucidate the PSI calculation in EXON Skipping? and the meaning of that in this splicing class? Thanks again

wososa commented 1 year ago

Hi @parsboy66 ,

Thanks for getting back to me. Any SES/MES/MXS events with a negative delta-PSI value means "exon-skipping". For example, if groupa contains normal samples and groupb contains tumor samples, a -20 means 20% exon-skipping is happing in the tumor samples.

Best, Woody

parsboy66 commented 1 year ago

Appreciate it woody for availability.

Regards