Maximum junction lentgh

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Olga Tsoy

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Mar 25, 2021, 8:29:35 AMMar 25
to majiq_voila
Hi,

maybe a strange question: is there a limitation on the size of a region that could be found skipped/retained? In other words, what is the maximal possible length of a junction?

Thank you!

Paul Jewell

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Mar 26, 2021, 11:40:01 AMMar 26
to majiq_voila
Hello, 

I've seen some junctions anecdotally which span nearly the entire gene. Majiq to my knowledge does not place a hard limit on maximum junction length. 

Thanks, 
-Paul

Aicher Joseph

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Mar 26, 2021, 1:13:15 PMMar 26
to Paul Jewell, majiq_voila

Just to add to Paul’s answer, MAJIQ will not assign a junction to a gene unless its start and end are within the gene’s starting/ending coordinates. So, in this sense, the longest possible junction that can be seen in quantifications/VOILA is determined by the longest (in genomic coordinates) gene.

 

Joseph

 

-- 

Joseph Aicher (he/him/his)

MD/PhD Candidate, GS6

Perelman School of Medicine

Genomics and Computational Biology Graduate Group

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