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A: How to download genome assemblies from NCBI with a list of GCA identifiers?
How to download genome assemblies from NCBI with a list of GCA identifiers?
Answer: Why is RNA-Seq library size not constant among samples?
Answer: TFs and Gene databases
Answer: java out of memory error through beagle for imutation
A: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
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Comment: A question about reference genome for creating the consensus sequence
by
me
• 0
Hi, thanks for your information. I am a bit confused now. Does this mean the cram file already contained reference genome information? I in…
Comment: PseudobulkExpression.Seurat error
by
Bastien Hervé
5.3k
> None of the requested assays are present in the object Does the assay `originalexp` exist in your object `seurat_from_cds` ?
Comment: identifying transgene insertion site in WGS
by
Cameron.walker9900
• 0
When calling for SVs using gridds, should I use the reference genome that I added my transgene to, or should I use the unedited reference?
Comment: Question regarding WGCNA
by
deepak
• 0
Thank for the reply. I am running this code: # set a set of soft-thresholding powers powers = c(c(1:20), seq(from = 22, to=30, by=2)) # Ca…
Comment: RNA seq analysis
by
prifa
• 0
thank you for your reply Zepper, a bit clarification, I took all the samples from SRA data table, but yes from different lab and also diffe…
Comment: RNA seq analysis
by
Matthias Zepper
4.6k
That you have a varying number of replicates is not ideal ([see here why][1]), but manageable. See for example the [Specific experimental d…
Comment: Percentage coverage of reference genome by de novo genome
by
Joe
21k
OK, in that case it should be even easier as its just a single pairwise alignment, so the same advice holds.
Comment: FarmCPU - how to explain the reported 'effect'?
by
chloek88
• 0
Hi Phillip, Did you ever figure out the answer to this? I also have rMVP results with a column 'effect', values ranging from ~-1.4 to +1…
Comment: Soft-clipping read ends based on read group
by
chenl
▴ 10
Hi, Can you please share how did you clip both ends of the reads with ClipReads? Clipping form the start with `-CT "1-3"` for instance wor…
Comment: Phasing a mixture of two individuals' DNA with long reads
by
njornet
▴ 20
This is related to that other question but for now, the only thing I'm interested in is separating the three unique chromosomes, without as…
Comment: A question about reference genome for creating the consensus sequence
by
GenoMax
142k
> I wonder how to adjust the base genome. If you are looking to make changes to the reference you used for alignment then look into http…
Comment: Phasing a mixture of two individuals' DNA with long reads
by
GenoMax
142k
We had a related discussion in a prior thread by OP: https://www.biostars.org/p/9593780/ Do you have genotype (or independent sequence) da…
Answer: TFs and Gene databases
by
b.contreras.moreira
▴ 180
I can also suggest <https://footprintdb.eead.csic.es> which links TFs to their DNA motifs, not their gene targets.
Comment: Correlation Analysis
by
manaswwm
▴ 510
How many methylation and expression values do you have per gene? If per gene you have a table named - *gene_corr*; which has two columns - …
Comment: How do I change the title font size in ViolinPlot (Seurat)
by
Assa Yeroslaviz
★ 1.8k
thx for the explanation. I did look at the function and I also read in the help page, that you get a patchwork object, only when using `co…
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