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Recent Replies
Answer: When is it advantageous to use a non-splice aware aligner like BowTie2 over a sp
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GenoMax
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> 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
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Rob
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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
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xingyu
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I met this problem, too. Is there a particular processing procedure?
Comment: Best BAM viewer in 2022
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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
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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
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> 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
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The models LRT tests should be nested, here you compare two different models which could be very different.
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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
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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…
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That is exactly what I was looking for! Thank you!
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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
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You can run tools like [SnpEff][1] or the [Variant Effect Predictor][2].
I trust you have performed steps like base quality score recalib…
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*(Disclaimer: I have no expertise in interpreting genetic variants, but the issue aroused my scientific curiosity)*
According to [dbSNP,][…
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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…
Answer: Annovar and the 'Otherinfo' column in VCF inputs
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tayebeh.ranjbar1992
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Hello, I also got the same error as you. " Error: the last column in header row should start with 'Otherinfo"
Did you manage to fix this e…
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