What command sequence should be followed to run MAJIQ to analyze long reads of long data?

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Jiaxin Zhao

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Aug 29, 2024, 9:10:36 PMAug 29
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Dear MAJIQ Development Team:

Greetings! I have some more questions about MAJIQ for analyzing long read length data:

When MAJIQ is used to analyze short-read-long data, it has gone through build, deltapsi (the mode I chose for quantify), and voila modulize, and I see from your “MAJIQ-L” documentation that there are two commands specific to long read-longs volia lr, majiql.

As I understand it, analyzing long length data should be done in the following order (similar to short read long data):
1. build (get .majiq file for deltapsi);
2. deltapsi;
3. voila modulize;
4. if you need to compare long and short read length data, you can choose to run volia lr, majiql in that order.

May I ask if I understand this correctly? If it is not correct, how should I analyze deltapsi for long read long data? (Compare the difference between the two groups)

Best,
happypiggy

San Jewell

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Sep 4, 2024, 11:14:13 AMSep 4
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Hi Happypiggy,

At the moment, we don't have a well-established way to calculate deltapsi between two long read datasets in a rigorous enough manner for our satisfaction, therefore, the Majiq-L visualization is currently only available for use with majiq PSI inputs. This is due to being able to show a fair comparison between the short read and long read data. There is a patch in the works for voila, in the next release, which will allow dPSI and HET inputs, but show a "fake" LR dpsi. This will be for convenience of using majiq dPSI inputs with LR data, rather than a rigorous LR dpsi definition at this time.

For the current usage I would recommend using majiq PSI inputs, possibly with a second $ voila view instance running side by side to show your dPSI version as well.

Let me know if it makes sense,
-San

Jiaxin Zhao

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Sep 12, 2024, 4:43:08 AMSep 12
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Hi San,

Sorry for the late reply, now I'm trying the method you said, so far I've followed the process of dealing with short reads of long data to deal with long reads of long data, please allow me to come back and communicate with you when I encounter problems in the future~ 
Have a nice today !

Best,
happypiggy

San Jewell

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Sep 16, 2024, 1:03:41 PMSep 16
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Hi Happypiggy,

No worries. Please create a new topic if the general question is different. I hope you have success!

-San
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