18 votes
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What is the difference between a Bioinformatics pipeline and workflow?

Great question! Note that from a prescriptive standpoint, the terms pipeline and workflow don't have any strict or precise definitions. But it's still useful to take a descriptive standpoint and ...
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6 votes
Accepted

Can blat use more than one core/CPU to speed up the alignment?

BLAT can only use one CPU. It is actually not the right tool for full-genome alignment. For "two versions" of the same species, MUMmer and minimap2 are orders of magnitude faster and probably give ...
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  • 5,645
4 votes
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Genome assembly of SRR12196449 with SPAdes

Update 2: I looked into this a little more, with the various data sources. This is related in part to the answer submitted by OP juanjo75es, in addition to discussion on chat. I don't entirely ...
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4 votes
Accepted

Running a script in python

You are trying to run a script file in the python console. That doesn't make sense. The console is for running commands manually, interactively. A script is a collection of commands. You can't just ...
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  • 7,957
2 votes
Accepted

Codon usage analysis for whole genomes

This python script will remove all stop codons from your fasta file. I called it remove_stops.py ...
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  • 3,041
2 votes

BUSCO does not find buscos in reference sequence of C. elegans (technical problem)

Most likely your Augustus installation is not functioning properly. Did you install Augustus from source or using conda? I believe the conda version of Augustus is known to have some issues. ...
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2 votes

How to show bootstrap values on a phylogenetic tree constructed with RAxML

Depending on the search parameter settings RAxML produces several output files among which you normally find: RAxML_bipartitions.result: If you used the ­-f b option, this file will contain the ...
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  • 21
2 votes
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What is the perferred method of optimization or energy minimization of small molecules downloaded from PubChem?

The difference between different force-fields is not going to be major, it is the side steps which are. When If you are starting from a SMILES string, optimisation is a must obviously. If you are ...
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  • 3,434
2 votes
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What is the file .mums created by mummer?

Maximal Unique Matches To answer the question about MUMs, there are two important definitions: A "match" is maximal if it cannot be extended in either direction and still be a match i.e, ...
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2 votes

Genome assembly of SRR12196449 with SPAdes

After many considerations, I am going to accept the response from Maximilian Press. I see now that some viruses have high variability (HIV even 50% of the sequence). Therefore MN630242.1. and U11820.1 ...
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1 vote

Permanent error in installing R package

try devtools::install_github('linxihui/NNLM'), if it doesn't work you need to install the gfortran binary on Mac. If it still doesn't work, try to upgrade to 4.0....
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1 vote
Accepted

A box plot of qualitative variables

I'm not sure that boxplot will be the more appropriate representation, as you will end with two numbers (count of Clonal and SubClonal) per groups of patients. One solution will be to first create a ...
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  • 1,021
1 vote
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Interpreting quantitive outputs from maximum likelihood phylogenetic trees

In summary, RAxML_bipartitions.output_bootstrap.tre Is the only file of interest. The reason this is true in this context is really complicated and you have to ...
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  • 6,977
1 vote
Accepted

How to show bootstrap values on a phylogenetic tree constructed with RAxML

Apologies for the delay. The calculation is a majority consensus phylogeny of a maximum likelihood bootstrap, which is superimposed into a maximum likelihood phylogram. That's the tech. speak over ... ...
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  • 6,977
1 vote

AutoDock 4 -soft docking

The smooth parameter is an optional keyword and command that changes the smoothing potential. If not provided, the default is 0.5 angstroms by default. Try passing ...
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  • 1,119
1 vote

Plot a circos plot to show the consistency between 2 samples

A circos plot is most likely not the most appropriate solution here. What I would suggest is a confusion matrix, of which you can find an example here: For every variant in your vcf you'll add a ...
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1 vote
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How do I tell featureCounts to ignore fragments that overlap with more than one feature?

If a fragment overlaps multiple genomic features then it's unassignable, which is the appropriate way to handle ambiguous mappings when the resulting counts are then given to tools like DESeq2.
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