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Comment: Integration of RNA seq data aligned to different reference genome versions
by
Ram
38k
It should be trivial to realign. Integrating cross-genome datasets can introduce errors and I think it's worth the realignment effort to el…
Comment: ClusterProfiler : What is GeneRatio and BgRatio?
by
Rene
•
0
genes <- letters[1:15]
gs_df <- data.frame("gs_name"=c(rep("genesetX", 10), rep("genesetY", 25)),
"entrez_g…
Comment: FeatureCounts >edgeR > GO
by
Pegasus
▴
80
Thank you Basti.
I annotated my genome using NCBI annotation tool, so I believe I should use the NCBI database.
However, the gene_IDS l…
Comment: Suggestion for approaching multiple conditions scRNA-seq
by
Eisuan
▴
20
Hi,
I analyzed the datasets separately as follows:
- control+condition 1
- control + condition
1+2 (not all the three merged!)
I applied…
Comment: Update MitoZ 3.4 to 3.5
by
Ram
38k
Right, that is one interpretation. Another is that they wish to replace the existing version and not add a new version, as most users new t…
Comment: Quality control of Chip-seq data (NRF and PCB)
by
Darked89
4.2k
If you remove the duplicates then the non-redundant/non-duplicated fraction will be 1.0. But if you save the log file during the de-duplic…
Comment: Update MitoZ 3.4 to 3.5
by
Darked89
4.2k
Well, the author asked for "update without uninstall", so I assumed he/she wants to keep the 3.4 version for the time being.
Comment: Suggestion for approaching multiple conditions scRNA-seq
by
ATpoint
70k
"performed on Seurat" is like saying that the repair was done with a hammer and skrewdriver. Seurat has plenty of functions, you need to be…
Comment: Update MitoZ 3.4 to 3.5
by
Ram
38k
While this installs a conda environment with mitoz 3.5, it does not technically update the existing installation. Please note that this (i.…
Answer: Update MitoZ 3.4 to 3.5
by
Darked89
4.2k
conda create -n mitoz_35
conda activate mitoz_35
conda install -c bioconda mitoz
**EDIT**
you can also use Singularity conta…
Comment: What is the NCBI's definition of an "atypical genome"?
by
GenoMax
127k
You probably need to ask NCBI Help desk for an authoritative answer. Post their response when you get one here.
Comment: How to limit the use of RAM for clustalo?
by
animeshizik
•
0
Hello, thank you for responding to the problem!
My work computer has 32GB of RAM. I was running an alignment for a 5000 genome monkey pox…
Comment: Suggestion for approaching multiple conditions scRNA-seq
by
Eisuan
▴
20
Hi! Two biological replicates. The previous analysis has been performed on Seurat.
Comment: genome annotation [sstart] [send] - how to get protein sequence from gene
by
danfarkas
•
0
Hi shenwei356,
Thanks for the clarification. That makes sense.
I also realised that the reason I was confused, is because I need to also …
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