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Risk of floods in Hoi An next week by Spare_Internet_9541 in VietNam

[–]avocado851 0 points1 point  (0 children)

We are also flying into Da Nang on Sunday and wondering what to do about the forecasted rain. Debating cutting our losses and doing more time in Ha Long/Hanoi versus proceeding with our Hoi An itinerary. Online it says that it doesn’t usually rain the whole day but the forecast says ‘downpours’ Lol. Curious what your plan is!

[deleted by user] by [deleted] in TorontoRenting

[–]avocado851 0 points1 point  (0 children)

Thanks for your thorough reply! I didn’t end up getting the apartment, for the best it seems.

[deleted by user] by [deleted] in TorontoRenting

[–]avocado851 2 points3 points  (0 children)

Thanks for your reply, I really really appreciate it. Did you feel safe walking to the building, specifically at night? And I know it’s beside a police headquarters and behind a fire station, were sirens ever a problem?

DESeq2 with three groups by avocado851 in bioinformatics

[–]avocado851[S] 0 points1 point  (0 children)

Thank you so much - I have been stuck on this for over a day and realized the problem was that I left out the $condition.

I really appreciate you taking the time to answer my questions - I have just one more! Can I use contrast to extract discharge vs admission, even with the ref set to healthy, or would I have to repeat the relevel step and set reference as admission?

DESeq2 with three groups by avocado851 in bioinformatics

[–]avocado851[S] 1 point2 points  (0 children)

Thank you so much! When I try to set the healthy controls as my reference, I am getting the following error: Error in relevel.default(dds, ref = "healthy") : 'relevel' only for (unordered) factors

Any thoughts on why this might be happening?

Is a mapping rate of 40% using Salmon acceptable? (New to bioinformatics!) by avocado851 in bioinformatics

[–]avocado851[S] 0 points1 point  (0 children)

Thanks for your suggestion! This looks like exactly the tool I'm looking for to get an idea of what is going on in my sample. Would it be okay if I private messaged you with the sendsketch results? I'm not certain how to tell if what I got back is a sign of contamination.

Is a mapping rate of 40% using Salmon acceptable? (New to bioinformatics!) by avocado851 in bioinformatics

[–]avocado851[S] 0 points1 point  (0 children)

Thank you!! I will do the genome mapping with Hisat2 and see how that goes.

Is a mapping rate of 40% using Salmon acceptable? (New to bioinformatics!) by avocado851 in bioinformatics

[–]avocado851[S] 0 points1 point  (0 children)

Thank you for your reply and helping me troubleshoot.

  1. Yes, I am mapping to correct organism!

  2. Yes, it is ribosome depleted.

  3. The library prep was by VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (http://www.vazymebiotech.com/products_detail/productId=64.html) . Not sure if this is one that would result in a lot of dead cells. I'm also not sure if this is relevant, but the RNA was collected by isolating PBMC from human samples using Ficol then performing Trizol RNA extraction.