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Recent Replies
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
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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
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mbyvcm
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> 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
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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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I don't think there are any other records, including what you call canonical, for this protein.
Maybe this will help you, using [**Entrez …
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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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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
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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
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swbarnes2
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> or the Different sequence-type (paired vs single), difference in
> read-length (150bp-x2 vs 75bp-x1) will have any technical or batch
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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…
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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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Segfaults are related to memory, which is what part of the message is telling you. If you are running this job under a job scheduler make s…
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The problem was the filename suffix, it's meaningful in how IGV treats the file. It is .pk here, but changed to .bed and it works.
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