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Why employ normalization methods, and how can they be utilized in DEG analysis?
Comment: Help with running egsea()
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Comment: Bacterial plasmid analysis
The Biostar Herald for Monday, May 06, 2024
Comment: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C
Answer: Is therer any suggestions on mapping rate of WGBS data?
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Comment: Help with running egsea()
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Chris
▴ 260
Thanks 1769mkc! I tried this tool. Gene expression of 2 groups is just slightly different (not hundred of differential express genes). The …
Comment: Help with running egsea()
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1769mkc
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https://metascape.org/ this is one of the ways to make life easier if you have the genes already from the differential list
Comment: RNA editing sites based on DNA seq and RNA seq
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Ahiad Chen Zion
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In those unaligned reads, I am looking for hyper-editing. But the alignment should be much higher
Comment: Bacterial plasmid analysis
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GenoMax
142k
Once you have some of these basic issues sorted out you can create a `tools` post describing `pling`.
Comment: Bacterial plasmid analysis
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Daria
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Hi, you need to run it with `PYTHONPATH=<pling_path>` in front of the command (a bit clunky, I know -- will likely be fixed in the next ver…
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I don't think you can use N's in `literal=` since the match is literal as the option says. Depending where in the read this pattern is you …
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ATpoint
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> As such, I am wondering what the protocol is here? My personal suggestion is to just do it and see what comes out. Multiple comparisons …
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JACKY
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I've followed this [vignette][1] [1]: https://tanaylab.github.io/metacells-vignettes/iterative.html Which is the only pipeline that d…
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GenoMax
142k
https://www.biostars.org/u/98332/ : This may be best posted as a new question since you are now running into a problem with tool usage.
Comment: Differentail gene expression results
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ATpoint
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What is your question? See https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html which covers most relevan…
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Please post your solution as an answer.
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Please --- https://www.biostars.org/p/357878/ https://www.biostars.org/p/75548/ [Ten Simple Rules for Getting Help from Online Scientifi…
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carolofharvest
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If rRNA genes have been mistakenly assigned to these genes, could it be expected that the percentage of ribosomal genes(rpl,rps) would be …
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(+1) *"implementing" the method just using base R linear models.*: I find implementing from basic starting point to be one of the best, if …
Answer: Is therer any suggestions on mapping rate of WGBS data?
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Papyrus
★ 2.9k
Mapping rate for bisulfite data is typically worse because of reduced complexity of the sequences. The efficiency will depend on your read …
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