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mhalushka / miRge

miRge - microRNA alignment software for small RNA-seq data, now at v2.0
GNU General Public License v3.0
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Difference between a zero count and an absent record in miR.Counts.csv? #20

Open AaronHechmer opened 5 years ago

AaronHechmer commented 5 years ago

I've just run miRge2.0 across 34 human samples, apparently with success, and I'm trying to understand the output. Unsurprisingly, many miRNA have a count of zero. However, sometimes a count will not be provided at all for some subset of samples where it is zero for another subset. What's the difference, in terms of miRge2.0's workflow, between a count of zero and a miRNA not being included at all in the final record keeping?

Thanks for the good work!

mhalushka commented 5 years ago

That's a great question. A zero and a missing value are equivalent. A missing value should be a 0 as well. I've checked it. It's some oddity of the code that I can't quite figure out but I'm hoping my new postdoc will be able to solve it and fix it. As you've done multiple runs, just be careful merging them together.

AaronHechmer commented 5 years ago

Thanks and thanks for the quick reply... yes, I noticed the discrepancy while merging the counts into a single matrix.

From: Marc Halushka notifications@github.com Sent: Friday, March 29, 2019 1:19 PM To: mhalushka/miRge Cc: Hechmer, Aaron; Author Subject: Re: [mhalushka/miRge] Difference between a zero count and an absent record in miR.Counts.csv? (#20)

That's a great question. A zero and a missing value are equivalent. A missing value should be a 0 as well. I've checked it. It's some oddity of the code that I can't quite figure out but I'm hoping my new postdoc will be able to solve it and fix it. As you've done multiple runs, just be careful merging them together.

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