About negative numbers in the "spliced_with_coord" column in the Voila Modulizer output

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Shengwei Xiong

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Jan 15, 2024, 12:21:53 PMJan 15
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Hello all,

I encountered an issue while working with the Voila Modulizer output, specifically related to negative numbers in the "spliced_with_coord" column. Are those simply bad lines?

Best,
Shengwei
Screenshot 2024-01-15 at 12.20.15 PM.png

San Jewell

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Jan 17, 2024, 9:49:13 AMJan 17
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Hi Shengwei,

I might need to see the rest of the file but I'm guessing the exon in these lines is a half exon, and thus doesn't have a start coordinate. If this is not the case then it sounds like it might be a bug. Can you confirm? See here for information about half exons: https://biociphers.bitbucket.io/majiq-docs-academic/getting-started-guide/faq.html

Thanks,
-San

Shengwei Xiong

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Jan 17, 2024, 11:55:29 AMJan 17
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Hi San,

I don't think it is a half-exon problem. I have attached the TSV file. Could you take a look? Thank you!

Best, 
Shengwei

alternate_first_exon_negative.tsv

San Jewell

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Jan 22, 2024, 3:25:25 PMJan 22
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Hi Shengwei,

I recently ran modulizer over one of our larger sets of gtex cancer data as a wide-scope test, using the same arguments you provided. Looking at alternate first exon output I wasn't able to reproduce this kind of issue / result. Therefore I feel that there must be some kind of weird unexpected splicegraph situation happening in the data that you are working with. Based on your security / privacy principals, would you have any issue sharing your data set (splicegraph.sql, sj/majiq/voila files) with me for debugging purposes? I can provide a secure place to sftp upload the data if you decide to proceed.

Thanks,
-San
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