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Recent Replies
Comment: Different comparisons in RNASeq Analysis
by
mbyvcm
▴
460
The OP wanted to directly compare the Mutants (Analysis 3), and the analysis I have proposed for their consideration will do that, whilst c…
Comment: Should I perform integration to correct batch effects?
by
han
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Actually, I tried two methods—one with batch effect correction and one without—and the results were completely different.
In the UMAP witho…
Comment: Different comparisons in RNASeq Analysis
by
swbarnes2
15k
You cannot remove batch effects where they overlap perfectly with a biological condition of interest.
Comment: Different comparisons in RNASeq Analysis
by
swbarnes2
15k
That's not really the comparison OP was asking about, but I don't think they can meaningfully do the comparisons they wanted.
Comment: Different comparisons in RNASeq Analysis
by
swbarnes2
15k
You will get slightly different alignment with longer paired reads. You don't want that if you want to compare the two sets of reads to ea…
Comment: Distribution of assayed SNPs per sample
by
mbyvcm
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460
> According to my logic, one could do this by filtering out SNPs with missing genotype calls (./.), however when I did this, I ended up hav…
Answer: Different comparisons in RNASeq Analysis
by
mbyvcm
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For analysis 3, you could think about something like:
(Plant Mut vs. Plant WT) vs (Flask Mut vs. Flask WT)
In doing so you are internally…
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Mensur Dlakic
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I don't think there are any other records, including what you call canonical, for this protein.
Maybe this will help you, using [**Entrez …
Comment: Different comparisons in RNASeq Analysis
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jkim
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See [the post](https://www.biostars.org/p/403053/#473727).
Comment: Different comparisons in RNASeq Analysis
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SomeOne
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Hi. Thank you for replying.
If i trim the PE data to SE and at 75bp length, and perform the analysis.
Wouldn’t that effect the final co…
Comment: Different comparisons in RNASeq Analysis
by
SomeOne
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Hi! Thank you for your response.
Can you share some information on how to remove this batch effect ?
Answer: Different comparisons in RNASeq Analysis
by
swbarnes2
15k
> or the Different sequence-type (paired vs single), difference in
> read-length (150bp-x2 vs 75bp-x1) will have any technical or batch
…
Comment: Different comparisons in RNASeq Analysis
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jkim
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For analyses 3 and 4, you will need to account for batch effects, which I expect to be substantial given the differences between datasets—e…
Comment: Distribution of assayed SNPs per sample
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1769mkc
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if you can share some part of the data that would be helpful what you are trying and what the final output expected , that helps for people…
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That error is caused by a simple failure to open that file (which is created in the `vg prune`). Usually, that results from a typo in the f…
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