3
votes
Accepted
Which human reference genome version does VARAdb use?
They are using hg19.
I found this by simply going to "Browse" then copying taking the first rsID in the list (rs1891805) and comparing the chromosomal position they give in VARAdb to what I ...
- 9,662
3
votes
Accepted
Barrnap Bacterial rRNA Predictor script permission denied error when running Prokka
My suggestion is to run prokka from within conda by simply downloading miniconda then
...
M__♦
- 11.9k
2
votes
Identifying the promoter on the reverse strand using visualization software (seqmonk)
Have a look at this UCSC browser shot.
Looking at the WDR92 transcript, note that it is transcribed right to left. This would indicate that the promoter is on the right. Indeed, we see a variety of ...
- 3,794
2
votes
What is the best Query to retrieve DNA from NCBI?
There are two main problems I can see in your approach. First, gene names are not standardized across species and the "same" gene (what that means is a whole different discussion) can have ...
- 9,662
2
votes
Extract data from genome
This sounds like you are wanting to perform a machine learning calculation. However, for this question leveraging KEGG, Kyoto Encyclopaedia of Genome and Gene and building an SQL database around it is ...
M__♦
- 11.9k
1
vote
Accepted
What is the best Query to retrieve DNA from NCBI?
The search term you need is [gene name] rather than [title]. For example,
...
M__♦
- 11.9k
1
vote
How to interpret a GenomeScope plot?
Based on the numbers shown above the plot, and the appearance of the curve, this looks like reads from a diploid genome approximately 113Mb in length that was sequenced at around 174X coverage.
- 13.8k
1
vote
Why is there gene without annotated location?
This gene/protein appears to have been described exclusively as an isozyme / electrophoretic mobility assay of a protein.
See for example this PepC mutant page:
The Pepc locus controls ...
- 3,794
1
vote
Extract data from genome
I've used Augustus stand alone (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160219/) to find genes in a given eukaryotic genome. I agree you can then use things like KofamSCAN to categorize the ...
- 141
1
vote
Sanger sequencing annotation error
Just to give my thoughts:
The missing information is the actual sequence
Is this a conflict in the change in position of the insert?
Could it simply be a consequence of down stream numbering, either ...
M__♦
- 11.9k
1
vote
I have a partially described gene from a plant, which tool may I use for predicting regolatory and UTRs sequences from a single DNA fragment?
Assuming that you know the gene name, you would be able to look it up in a transcriptome assembly presumably, or perhaps NCBI has a full length transcript (search ...
- 3,794
1
vote
Problem with Seurat reference mapping
Yes! Multiome seems to have cells with much higher mitochondrial gene content. I don't understand the biology behind this. But in using a cut off of 5% (i.e. remove cells with >5% MT genes) I lose ...
1
vote
dog coordinates (canFam3) to human coordinates (hg19)
Based on this old answer, this is not recommended for liftOver. For between-species liftovers, it is claimed that you are likely to want a different tool such as pslMap. For a lot of rather detailed ...
- 3,794
Only top scored, non community-wiki answers of a minimum length are eligible