Questions tagged [software-usage]

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How to modify dot plot in MUMmer 3 for bacteria comparative genomics?

I was trying to make a dotplot to visualize genome-genome sequence alignment by using the MUMmer 3 software (it is typically used to compare whole genome sequences of bacteria). I runned the same ...
2
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2answers
56 views

What is the file .mums created by mummer?

I am doing genome sequence alignment using MUMmer, in particular I want to do a dotplot with mummerplot. So the passages that I did are: 1.create a file .mums with the following command line: ...
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0answers
103 views

Prokka error message

I am trying to run Prokka but the following error message appears: Could not run command: makeblastdb -hash_index -dbtype prot -in /cluster/software/prokka/1.13.7-gompi-2019a/db/kingdom/Archaea/sprot ...
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2answers
165 views

Genome assembly of SRR12196449 with SPAdes

I am trying to assemble the run SRR12196449 with SPAdes. The description of their project is: This project expected to standardize a method for amplification and ...
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0answers
21 views

Blast templates not found in PSI-TM Coffee

I'm trying to run psicoffe mode on Ubuntu 18.04, but it returns the error: 17633 -- WARNING: Impossible to find BLAST Templates Check that your blast server is properly installed [See documentation][...
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2answers
312 views

Permanent error in installing R package

I want to install NNLM ...
1
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1answer
91 views

What is the perferred method of optimization or energy minimization of small molecules downloaded from PubChem?

I will be docking a small library of molecules that I have downloaded from PubChem using AutoDock. I thought why not minimize their energy before docking using ChemDraw. I am thinking; what is the ...
1
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0answers
349 views

Create a genotype matrix from VCF file using bcftools

I have a vcf file that contains SNPs from chromosome 2 for 2000 samples. I want to create a genotype matrix from this vcf file. The file is in zipped format as well so that I can use ...
0
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1answer
44 views

A box plot of qualitative variables

I have 2 groups of patients; responders to chemotherapy and non-responders I have calculated cancer cell fraction (CCF) of a set of driver genes (by variant allele frequency) for each group and I ...
-2
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1answer
83 views

Running a script in python [closed]

I am trying to run a script in python but I getting this error ...
1
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1answer
135 views

Interpreting quantitive outputs from maximum likelihood phylogenetic trees

I ran a calculation in RAxML to determine the majority consensus phylogeny of a maximum likelihood bootstrap (How to show bootstrap values on a phylogenetic tree constructed with RAxML), and I got ...
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2answers
4k views

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

I apologize for this very basic question. With @Michael G.'s help, I have been learning how to use RAxML to build a phylogenetic tree (How to define an outgroup to build a robust amino acid tree) and ...
0
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1answer
29 views

AutoDock 4 -soft docking

How could I turn on/off the smooth potential in AutoDock4? I need to do two docking. The first one is soft docking with smooth potential and the second is re-docking without the smooth potential.
2
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0answers
29 views

How to interprete PlasmidSeeker results concerning plasmids?

I've been interested in plasmid detection in bacterial genomes. I tried plasmidfinder and this software found only one plasmid in each of my two bacterial genomes. I was dubious about these results, ...
2
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1answer
218 views

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

I am working on a GNU/Linux machine. I have installed BUSCO using conda. I have downloaded the nematode dataset nematoda_odb9.tar.gzhere. I downloaded the reference ...
0
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1answer
189 views

Plot a circos plot to show the consistency between 2 samples

I have called SNP and INDEL in two matched samples by strelka and extract this information from .vcf file and I have these ...
13
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1answer
2k views

What is the difference between a Bioinformatics pipeline and workflow?

I want to understand the difference between pipeline systems and workflow engines. After reading A Review of Scalable Bioinformatics Pipelines I had a good overview of current bioinformatics ...
0
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1answer
329 views

How do I tell featureCounts to ignore fragments that overlap with more than one feature?

I am using featureCounts from the subread package to count the number of fragments per gene in an RNA-seq experiment. I feed it a BAM file with paired-end reads aligned to a reference genome. In the ...
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0answers
70 views

BPGA - functional analysis

I have been using BPGA to perform pan-genome analysis on my set of isolates. Now, I need the functional analysis as well. However I am having problem with the function, as the program says I am ...
4
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1answer
260 views

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

I am using BLAT to align two versions of the genome of C. elegans. I can see in the Activity Monitor of my Mac Book Pro High Sierra that blat is using 100% of a CPU....
4
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1answer
68 views

Codon usage analysis for whole genomes

I am new to bioinformatics. So if these questions seem you to a bit childish please forgive me. I have two queries. I am intending to perform a codon usage analysis followed by correspondence ...
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0answers
34 views

Which secondary structure prediction algorithms don't query the PDB/DSSP for known homologous sequences?

There are several secondary structure prediction algorithms. I am interested in the algorithms which predict secondary structure without accessing the PDB to cheat by using the DSSP or STRIDE entry ...
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0answers
20 views

XCMS isn't evaluating the proper peak due to retention time drift

I'd like to do a targeted screening analysis for trace contaminates. However, due to the nature of the sample preparations, the retention times I'm getting drift a lot from run to run and XCMS isn't ...
1
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0answers
85 views

Mugsy error: Can't find species II dna at output/software/mugsy_x86-64-v1r2.3/mugsy line 501

I have installed mugsy in order to create a multiple genome alignment and a phylogenetic tree of several species of nematodes. The following command successfully pulls out the help: ...