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Recent Replies
Comment: getting exon coordinates
by
Pierre Lindenbaum
161k
https://www.biostars.org/p/385786/ ; <br> https://www.biostars.org/p/276608/ ; <br> https://www.biostars.org/p/411934/ ;etc...
<!--
How …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
GenoMax
142k
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
by
marco.barr
▴
120
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?
by
b.contreras.moreira
▴
180
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…
Comment: finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame
by
GenoMax
142k
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
by
Pierre Lindenbaum
161k
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
by
GenoMax
142k
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…
Comment: Can I perform a correlation test with 3 biological replicates per condition?
by
ATpoint
82k
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?
by
manuelmourato25
•
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?
by
ATpoint
82k
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
142k
> 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?
by
manuelmourato25
•
0
Thank you @atpoint . My apologies, maybe I should rephrase the question. I read the WGCNA docs already, and for the Pearson correlation tes…
Comment: How to extract cells of different species after mapping with combined genome?
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Can you confirm that this answer is specific for `singleron` technology and associated bioinformatics software.
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GenoMax
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What OS are you using? Are you able to run `blastn --help` and does it produce the in-line help?
> I used many query file.fasta
And tho…
Comment: Can I perform a correlation test with 3 biological replicates per condition?
by
ATpoint
82k
> However, even though 3 biological replicates per condition seems to be the norm in these experiments, many papers discuss that we need at…
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