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Comment: VEP won't show symbols for all variants; SnpEff will, but won't for others byRam 45k
Go with either, just mention which one you use and what version of it you're using. Personally, I go with VEP because it's been historicall…
Comment: Why protein sequence from AUGUSTUS can't find in blast byJl • 0
I used non-redundant protein sequence (nr) in blastp. Galaxy only allowed tick options and upload files, I didn't use hints and specify pre…
Answer: Co-expression analysis of miRNAs and target mRNAs byi.sudbery 21k
My vote in these situations is generally `rlog` or `vst`. They implement both library size normalisation and variance stabilisation. I woul…
Comment: fastq-dump: command not found, what is wrong? bycaidyn.c.j • 0
Hi, I am having this same problem as OP right now. When I do the echo $PATH command, it returns: /Users/chachonos/sratoolkit.3.0.0-ma…
Comment: Feedback Wanted: GenAnalyzer - Web App for Protein Sequence Analysis & Mutation bygenanalyzer24 • 0
You're right, thanks for catching that. Here it is: https://genanalyzer.pythonanywhere.com/. Let me know what you think :)
Comment: Gene Expression Timeline Analysis for N=1 byATRX ★ 1.2k
Thanks for all the inputs.
Answer: miRNA-seq: QC reports and workflow byGenoMax 150k
Since you have publications associated with this data (based on your last thread and a question before that) don't try to do this analysis …
Comment: Population genetics with mutect2 data byslzr_ • 0
Thank you so much, you were really helpful!Do you think it is possible to do some kind of analysis to evaluate positive selection or mainl…
Comment: Is there too little variation to detect meaningful gene changes? byswbarnes2 14k
I doubt your RNA quality is the issue. It's not likely that poor quality would cause reads to align to the wrong gene. Its far more likely …
Comment: Is there too little variation to detect meaningful gene changes? byMegan ▴ 50
The RIN values for these samples ranged around 6.0-7.0, which I think would suggest RNA degradation. From what I am aware of, I don't think…
Answer: Recommendations for Reference-guided de novo assembly assembly approaches or pip byshelkmike ★ 1.5k
You can do a de novo assembly and then scaffold the contigs using a reference by RagTag (https://github.com/malonge/RagTag). However, I per…
Answer: Per Base Sequence Content FastQC byshelkmike ★ 1.5k
The difference between (A or T) and (G or C) may reflect the GC composition of the genome. Thus, it is not indicative of some sequencing pr…
Answer: Seeking Advice on Handling Multiple Datasets for Differential Analysis in Transc byjared.andrews07 ★ 18k
What do you mean by "non-raw" data? You're correct in that grabbing arbitrary values on different scales and trying to mash them together i…
Comment: phylogenic analysis byRam 45k
None of the tags you used are relevant to the question you asked - they broadly describe the entire field of bioinformatics. I've fixed it …
Answer: Population genetics with mutect2 data byLauferVA 4.5k
Hi @slzr_In short, no. What I mean is, it’s generally not recommended to use Mutect2 calls directly for classical population genetics ana…
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