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This is my first question in the community.

I see the function FilterbyCoverage in Maser, and the explanation of average reads of the splicing events. When I get the results and view them I don't see how they are calculated. I'm using average reads = 5. I'm using Excel to verify the results manually and can't seem to match what Maser outcome indicates. Are the reads determined by each sample? Using rMATS output, IJC and SJC for each sample to determine reads? For instance if Sample 1 has IJC of 4 reads and SJC of 2 reads is that event removed due to the average being less than 5 or does this function add IJC and SJC together and this event would remain as a valuable event. Does the function look at all the reads for all the samples and take the average? I tried that in Excel and didn't get the same results as Maser in rMATS. Are the reads calculated based on comparison? The average of Wild Type samples to the Control samples and each has to be greater than 5? Some guidance would be appreciated.

I apologize if this isn't worded properly, I tried to be detailed in my question.

Excel detail of reads output

Jon Spring
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L Planco
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  • Please provide a minimal reproducible example. That includes a **minimal dataset** (just enough to demonstrate the problem), the **minimal** runnable code necessary to reproduce the issue, all necessary information on the used libraries. You can find more help in this post: [How to make a great R reproducible example](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example). – Jan Jul 05 '22 at 19:33
  • I’m guessing this needs both a [MCVE] and a `[bioconductor]` tag. – IRTFM Jul 05 '22 at 19:34

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