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Recent Replies
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
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Jeremy Leipzig
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We get this question like clockwork every 6 weeks.
I'll say it one more time:
**A freeze is a freeze.**
Patches are not a thing th…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
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ev97
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Thanks very much for your feedback! I will take all those things in consideration once I start the analysis!
Just out of curiosity, do yo…
Answer: getting exon coordinates
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ben@f
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A combination of bash and awk can do the work, suppose you have the gff file annotation of your gene of interest
and a text file with Gene…
Comment: getting exon coordinates
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https://www.biostars.org/p/385786/ ; <br> https://www.biostars.org/p/276608/ ; <br> https://www.biostars.org/p/411934/ ;etc...
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How …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
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I would have thought `needle` from EMBOSS would be the option to use.
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
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ok, then you should add the donor information to the PCA analysis. First create a separate dataframe for the donors, then add with `factor`…
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
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If you are willing to do some coding I think <https://github.com/smarco/WFA2-lib> is among the fastest global aligners, the repo has C++ ex…
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There is an API that you could try: https://www.ebi.ac.uk/pride/markdownpage/prideutilities
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
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thanks.
looks interesting but it's broken. the Firefox console shows a 404 for https://www.ebi.ac.uk/pride/ws/archive/v2/peptidesummary?ke…
Answer: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
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Perhaps: https://www.ebi.ac.uk/pride/peptidome/
This site is very slow. Almost to the point of being not usable. My search with your pepti…
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You're welcome. Yes, unfortunately you need quite a sample size for WGCNA simply because correlations with few samples are vastly underpowe…
Comment: Can I perform a correlation test with 3 biological replicates per condition?
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manuelmourato25
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0
Ah, I see. So seen that what I want is the per-gene correlation, the minimum of 20/25 for the pearson correlation still applies.
Thank you …
Answer: Can I perform a correlation test with 3 biological replicates per condition?
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ATpoint
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I think you're misunderstanding some concepts here.
WGCNA is a framework that defines modules based on how and which genes are correlated …
Comment: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
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GenoMax
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> most up-to-date build
Major build of the genome remains GRCh38. What you are looking at is the latest patch release for that build. Only…
Comment: Can I perform a correlation test with 3 biological replicates per condition?
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manuelmourato25
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Thank you @atpoint . My apologies, maybe I should rephrase the question. I read the WGCNA docs already, and for the Pearson correlation tes…
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