Questions tagged [software-usage]
The software-usage tag has no usage guidance.
26
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Changing transparency of markers in Chimera X
I am using the software Chimera X to visualize the 3d composition of molecules. I am very new to Chimera and only use it for visualization. The files I'm using are cmm files (xml-formatted) basically ...
- 11
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0
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12
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How can I use REMO tool to generate seq.dat and seq.txt files?
I am trying to generate seq.dat and seq.txt files myself, so that I can use them with REMO.
I am using ...
- 634
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41
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Applying colocalization analysis in Asian populations
I am planning to add colocalization method as a post-GWAS analysis in my study which is solely based on east Asian populations. I have noticed that coloc, enloc and eCaviar are being commonly used for ...
- 21
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334
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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 ...
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2
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241
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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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0
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440
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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 ...
- 11
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2
answers
309
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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
...
- 359
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2
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609
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1
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360
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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 ...
- 25
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711
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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 ...
- 341
1
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1
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53
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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 ...
- 1,951
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1
answer
155
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Running a script in python [closed]
I am trying to run a script in python but I getting this error
...
- 1,951
2
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1
answer
342
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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 ...
- 113
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2
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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 ...
- 113
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1
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31
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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.
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35
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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, ...
- 21
2
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1
answer
252
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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 ...
- 2,459
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1
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287
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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
...
- 1,951
14
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1
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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 ...
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448
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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 ...
- 2,459
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123
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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 ...
- 11
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1
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319
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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....
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4
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122
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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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38
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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 ...
- 507
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21
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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 ...
- 111
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113
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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:
...
- 2,459