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Recent Replies
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.
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…
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
•
0
Thanks for pointing out. Let me explain:
I had VCF files with gnomad 2.1.1 variants (chromosome positions). I performed a liftover with Pi…
Comment: STAR Intron Motif Script Gives Segmentation fault Error
by
Y
•
0
I still get the error:
line 65: 29089 Segmentation fault
I am not sure why this is occurring.
Comment: Dealing with transcriptome sequences that are smaller than their respective gene
by
GenoMax
134k
Align your data to one of the genomes available at NCBI. There is no way your strain is completely different than the common reference. If …
Comment: Chromosome bias on RNA-Seq differential gene expression analysis
by
blz
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20
I highlighted all the genes from that chromosome in the volcano plot and, as you can see below, many genes are below threshold of p-value a…
Comment: Chipseq analysis on repeat genes
by
pb11
▴
10
I tried that method and I am unable to capture that. I see in my RNAseq that repeat elements are enriched and we I see the chipseq marks ov…
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