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Recent Replies
Comment: Find potential important genes from bulk-RNA seq experiment
by
Michael
53k
There is no exact number but something around 15 to 20 samples is what I have read.
>Is there anything I can do to help with your work? …
Comment: Find potential important genes from bulk-RNA seq experiment
by
Chris
▴
180
Thanks @michael! So to do WGCNA, what are the minimum of control and diseased? Is there anything I can do to help with your work? I am happ…
Comment: Find potential important genes from bulk-RNA seq experiment
by
Michael
53k
In summary, you 3 samples plus 1 control, the technical replicates do not help here. That is unfortunately not enough for WGCNA and only ba…
Comment: Weirdness in annotation (missing allele frequencies)
by
Ram
40k
You performed a liftover on your VCF and then used a liftover-gnomad211 for the annotation? Why not simply use the regular gnomad211 with y…
Answer: Highly inflated p-values in GWAS by regenie
by
LChart
3.3k
You don't appear to be specifying a covariate file anywhere. Are the other groups also excluding potentially confounding information like s…
Comment: Highly inflated p-values in GWAS by regenie
by
Ram
40k
> with a suggestion rather than an answer
Yet you chose to add an answer rather than a comment. I've moved it to a comment now, please be …
Comment: scRNAseq Differential expression analysis
by
Ram
40k
I want to believe this but then it's from everything-except-kallisto-is-bad Lior so I don't know how to feel about it.
EDIT: And of course…
Comment: High amount of intronic/intergenic reads in SMARTer stranded total bulk RNAseq
by
dsull
★
4.6k
Sounds like genomic DNA contamination to me. Even if you had captured nascent (unspliced) RNA, you should still have a much higher coverage…
Comment: scRNAseq Differential expression analysis
by
dsull
★
4.6k
My personal pessimistic opinion: Just do whatever you want. Differential gene expression in scRNA-seq is broken anyway.
https://twitter.co…
Comment: STAR Intron Motif Script Gives Segmentation fault Error
by
Ram
40k
You're running out of memory. I've never done this, but try using a better `--genomeLoad` option. See this post: https://www.biostars.org/p…
Comment: Find potential important genes from bulk-RNA seq experiment
by
Chris
▴
180
Hi @michael. I looked for tutorials that do WGCNA analysis and their input data are not very similar to my data. The data tutorial at https…
Comment: EMBL-EBI virtual course | Introduction to RNA-seq and functional interpretation
by
Ram
40k
1. Please put some effort into formatting your post, don't just copy paste from a web page. Reading a wall of text is hard and your reach w…
Comment: Dealing with transcriptome sequences that are smaller than their respective gene
by
langziv
▴
50
I have aligned the RNA to the strain's genome from NCBI. The issue is that some RNA sequences that match CDSs from the genome, match them p…
Answer: How to find out what adapters to remove after FastQC of RNAseq data?
by
GenoMax
134k
You can use bbduk.sh from BBMap suite (https://www.biostars.org/p/175003/#175005 ) or `fastp` to figure out what potential adapter sequence…
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