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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 discuss how the terms are commonly used in the bioinformatics community. But before talking about pipelines and workflows, it's helpful to talk about programs and ...


6

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 better alignment. EDIT (moving comment to answer): OP comments that the purpose of this alignment is for lifting over annotations using the UCSC PSL-based ...


4

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 understand the logic, but the general thrust seems to be that SPAdes makes weird assemblies somehow. Some notes that I made: REFERENCE ASSEMBLIES FIV sequence U11820....


4

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 run that by name in the console. If you want to use it, copy the contents of your script and try to run them in the console. The way you run a python script ...


2

This python script will remove all stop codons from your fasta file. I called it remove_stops.py #!/usr/bin/env python3 import sys from Bio import SeqIO stop_codons = ["TAG", "TGA", "TAA", "UAG", "UGA", "UAA"] fasta_it = SeqIO.parse(open(sys.argv[1]), 'fasta') for fasta in fasta_it: name, sequence = fasta.description, str(fasta.seq) try: ...


2

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. Something worth trying: Running a complete busco install in a VM. This image has all dependencies installed and properly configured.


2

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 input tree with confidence values from 0 to 100 drawn on its nodes! It is also printed when -f a ­x have been specified, at the end of the analysis the ...


2

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 using a 3D conformer from PubChem or even an actual sub-1 Å crystal structure from CSD, optimisation is nice for consistency. Which MMF94 is a solid choice. ...


2

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, for two strings $s,r$, a match $s_i,...,s_{i+k}$, $r_{j},...,r_{j+k}$ is maximal if $s_i,...,s_{i+k+1}$, $r_{j},...,r_{j+k+1}$ is not a match and $s_{i-1},...,s_{...


2

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 are apparently two strains. There are things I still don't understand but these are beyond the initial goal of my question. Concretely: Why SPAdes returns one ...


1

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 4.0.0. When you have this kind of trouble, look at the issue page of the github page. You will almost always see that others have had the same issue.


1

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 new categorical variable based on CCF values using for example ifelse statement for example by writing: df$Clonal <- ifelse(df$CCF > 0.95,"Clone","...


1

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 understand the statistics of likelihood and how they are interpreted within phylogeny to understand why. This file is simply the final output of a non-parametric bootstrap analysis performed by ...


1

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 ... the command is, raxmlHPC -f b -m PROTGAMMAILG -n output_bootstrap.tre -t RAxML_bestTree* -z RAxML_bootstrap.result RAxML_bestTree* = your maximum likelihood ...


1

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 0 with this keyword in the AutoGrid Parameter File to turn off smoothing potential. See the AutoDock 4.2.5 documentation for more details.


1

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 number in this matrix. One sample is the columns, the other is the lines. If your variant is homozygous in both, then you add in that square +1 (the cell with 5845 ...


1

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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