question about using STAR-aligned reads and MAJIQ to detect cryptic exons

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Daniel Fass

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Jan 17, 2024, 4:43:53 PMJan 17
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Dear MAJIQ team,

I am about to run STAR to align reads from a set of samples, in a subset of which I have a strong basis for suspecting the presence of aberrant cryptic exons based on previously published papers. I am planning on running STAR using Alexander Dobbin's 2-pass protocol which is said to have significantly increased sensitivity for detection of novel splice junctions. I am planning to use the options --alignSJoverhangMin 8 after seeing this recommended in this group, and  --sjdbOverhang 99 (my reads are 100). I'm wondering if you could suggest any other options to employ to maximize sensitivity for detection of cryptic exons, or is what I have indicated here sufficient?

Thanks very much,
Dan

Daniel Fass

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Jan 18, 2024, 12:48:43 PMJan 18
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Sorry forgot to specify that my plan is to try to identify differential novel splicing across several sets of samples (aligned by STAR) using MAJIQ, and I just wanted to ask about the optimal output from STAR to maximize detection sensitivity in MAJIQ.

Matthew Gazzara

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Apr 5, 2024, 8:00:04 AMApr 5
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Hi Dan,

Sorry I just saw your message but the protocol and options you described should be fine for detecting novel junctions with STAR.

Once you get to the MAJIQ builder stage there are a number of heuristics MAJIQ to determine if certain junctions are reliable and quantifiable (e.g. number of times the junction was seen, what fraction of samples in an experimental group had that junction, etc.) so it is worth checking out the help message and adjusting these parameters as you see fit. 

-Matt 
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