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
3
votes
Accepted
Problem installing RATT
Usually the home of a program is where the executable is. In order to make the system aware you need to include it as a variable when the terminal is run.
So you need to add it to the file at ...
- 4,693
2
votes
Is there anything similar to GSEA for locus-based (instead of of gene-based) data?
I tinkered with a program GSEA-SNP quite a few years back, which claims that it does a similar ranking procedure with SNPs. It carries out its procedure by first linking SNPs with genes, then running ...
- 13.8k
2
votes
Find specific functional genes from a list?
BioMart. Filter by your list of genes and a GO term linked to acetyl transferase activity.
- 1,749
2
votes
where to find pathogenicity metadata for E.coli genomes
you can use BacDive. This is the largest database for bacterial metadata.:
https://bacdive.dsmz.de/
e.g. you can search for the sequence accession "NCTC8196" and you would get the metadata of the ...
- 21
1
vote
PANTHER FUNCTIONAL CLASSIFICATION in R
One approach is to get the gene's sequence (DNA/AA) and use the interproscan API (e.g., https://www.ebi.ac.uk/Tools/common/tools/help/index.html?tool=iprscan5) with the httr2 library in R to POST ...
- 11
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
Bulk protein annotation with Prokka
Prokka doesn't need whole genomes, I've definitely used it for smaller contigs before so I think you're fine!
- 449
1
vote
Functional Annotation vs Functional Enrichment--which one should I use for Network Analysis?
The answer to your main doubt about "annotation vs. enrichment" is that you need both, but you already have one annotation.
You can only perform a functional enrichment analysis after you ...
1
vote
Differential Expression
I guess plasmodium doesn't have that many online tools dedicated to it so you can use the annotation packages from bioconductor and try it. I used clusterProfiler for analysis and org.Pf.plasmo.db for ...
- 1,678
1
vote
Accepted
Why are my genes filtered for Gene Ontology term enrichment?
What is "click here for details" saying? That link should contain an explanation of what happened.
GSEA usually requires entrez_id to run. If your list contains <...
- 547
1
vote
Compare functional enrichment between genelists
To compare gene list based on gene ontologies you can use GOSemSim (Note, I'm a contributor to the package). You can select the semantic similarity to compare them, that is how the redundancies and ...
- 4,693
1
vote
Accepted
SnpEff gene annotation with @ such as PCDHB@
The @ at the end of a name denotes a "gene cluster in chromosome region". This is mentioned in the official HUGO nomenclature guidelines in the "Characters reserved ...
- 9,662
1
vote
Accepted
RNA seq fasta file annotation from alignment to reference matches
An awk approach (assuming your input "csv" file is space-separated):
...
- 9,662
1
vote
Accepted
Why does RATT create a directory with chromosome sequences and how can I stop it?
RATT seems to be a very simple wrapper script that unfortunately does not clean up its temporary files properly. Short of modifying the code yourself, your only option is to perform the cleanup ...
- 4,845
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