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Recent Replies
Comment: Best BAM viewer in 2022
by
Cornelius
•
0
Thanks. This is always opinion based but I just don't want to miss the obvious one. I find IGV's UX could be better: no sideways scrolling,…
Answer: When is it advantageous to use a non-splice aware aligner like BowTie2 over a sp
by
GenoMax
122k
> aligners for short RNA-seq reads
If you are referring to microRNA (or any other cases where you don't expect the entity to be spliced …
Comment: When is it advantageous to use a non-splice aware aligner like BowTie2 over a sp
by
Rob
5.6k
Well, what about if you are aligning to the transcriptome rather than genome, or to a de novo assembled transcriptome?
Answer: GISTIC 2.0.23 error
by
xingyu
•
0
I met this problem, too. Is there a particular processing procedure?
Comment: Best BAM viewer in 2022
by
GenoMax
122k
No precise way to define "best". IGV is probably the "go to" viewer for most. There is IGB, Tablet, [ASCIIGenome][1] (text based), BAMView …
Answer: FigTree and ggtree
by
Cornelius
•
0
You can put emojis instead of names! I made this in `figtree` for example, the branch labels are emojis. You're a bit limited by emojis but…
Comment: Quality All Low in VCF Files
by
Pierre Lindenbaum
150k
> used this pipeline:
bwa aln ? this is an old pipeline unless you're working with short reads (length<50-70).
did you run any QC on t…
Comment: why do i get much more significant genes and wierd volcano plot with DESeq2 for
by
Asaf
9.4k
The models LRT tests should be nested, here you compare two different models which could be very different.
Comment: why do i get much more significant genes and wierd volcano plot with DESeq2 for
by
ATpoint
66k
Adding on that, using `~0+...` is non-standard in DESeq2, I am unsure how this plays with the LRT in combination with the reduced model. My…
Answer: When is it advantageous to use a non-splice aware aligner like BowTie2 over a sp
by
ATpoint
66k
There is none. Splicing is why these sort of aligners have been developed. You should provide a source for such a quote. It is not standard…
Comment: Determine type of mutation
by
kirillkirilenko.tomsk
•
0
That is exactly what I was looking for! Thank you!
Comment: WGCNA: minModuleSize is not responding correctly
by
andres.firrincieli
2.9k
You can use `intramodularConnectivity` to calculate the connectivity of genes and identity the top hub in each module (gene with the highes…
Answer: Determine type of mutation
by
Matthias Zepper
2.2k
You can run tools like [SnpEff][1] or the [Variant Effect Predictor][2].
I trust you have performed steps like base quality score recalib…
Comment: allele frequencies interpretation
by
Matthias Zepper
2.2k
*(Disclaimer: I have no expertise in interpreting genetic variants, but the issue aroused my scientific curiosity)*
According to [dbSNP,][…
Comment: Trouble when installing arb
by
krmoon518
▴
20
thank you for your comment!
yes, i am aware that it means that "arb_ntree" is missing in the bin/ folder. I followed the readme instruction…
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