Questions tagged [simulated-data]
The simulated-data tag has no usage guidance.
19
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Generate simulated bam for certain snps
I want to benchmark my DNA sequencing pipeline. In order to do that I want some gold-standard files in every step(.vcf,.bam,.fastq). I want to generate/simulate a bam file of reads for a given set of ...
- 295
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24
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Generating simulated gold standard NGS dataset/ Any publicly available smal gold standard NGS dataset
I am trying to check my variant generation pipeline for humans. The pipeline is for NGS. I am searching for any dataset(.fastq+.bam+.vcf) for any specific sample. Now, GIAB has a nice dataset for that....
- 295
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30
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Protein-Protein Simulation using Gromacs
Can we do protein-protein simulation through Gromacs? if yes, can anyone teach me the correct procedure to get this done.
Thank you,
1
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0
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48
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How to identify all descendents of a branch on a phylogeny
I'm trying to simulate the evolution of binary traits on phylogenies in R to end up with a dataset of the traits held by each tip. Starting at the root, at every timestep, new traits are added with a ...
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20
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Simulation software recommendation to confirm pipeline validity
I'm trying to detect convergent evolution in different samples of the same species.
I'm just trying to see if past 20 generations the nucleotide frequency of snps under pressure converges somewhat for ...
- 249
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16
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Can I use Aho-Corasick for epidemic spread simulation?
I found that with this string-finding algorithm, this algo can determine if a string(person) holds something(if he has sick, already got vaccinated, and et cetera.).
I am trying to simulate an ...
1
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1
answer
72
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building complex drug-dna for AMBER software
I will appreciate if you can please clarify some of my doubts about drug-DNA complex.
I want to study the drug-DNA simulation using AMBER. I did go through all the tutorials video on youtube but ...
3
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1
answer
114
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GROMACS Coordinates and velocity and force trajectories do not match accuracy
I am using GROMACS to perform MD simulations of proteins. So, I tried to record the simulation results nstxout, nstvout, and <...
- 195
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1
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108
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What are the units for the force output by nstfout, the velocity output by nstvout, and the coordinates output by nstxout in gromacs?
What are the units of force, velocity, and coordinates output by gromacs trajectory? In .mdp, they are specified by nstfout,<...
- 195
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2
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60
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How to modify DNA evolution model to fit actual data?
I'm working on understanding the evolution of a gene in a phylogenetic tree. I know the rates of evolution of each organism (from the tree).
I am taking a random DNA sequence with my gene, evolving it ...
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1
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404
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How to simulate phenotype from real genetic data for GWAS purpose?
I'm trying to simulate binary phenotypes from the 1000 Genome Phase 3 datasets using gcta64 --simu-cc, but no success.
Everything seems to be going well, but in the end I get:
...
- 207
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answer
76
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Simulating 3' end tag-based scRNA-seq reads
Are there any tools that will simulate 3' end tag-based single-cell RNA-seq reads? For example, Drop-seq, 10X Chromium, ...
- 631
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answer
84
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RSVSim insertions from chr1 to chr2
edit explaining python tag
I would still rather have a solution based on the RSVSim package in R, but while waiting for someone who might have an answer I wanted to look at other solutions as well.
...
- 153
5
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2
answers
1k
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How to simulate nanopore reads?
I have looked already here: Tools for simulating Oxford Nanopore reads
. This doesn't answer my question, because it lists a few Nanopore read simulators, but I have specific problems with each of ...
- 153
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3
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123
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Sampling haplotypes
I am trying to simulate different genome of peoples, I have data (VCF files) of various genes from the 1000K Gene project.
I want to simulate different whole genomes i.e generate a new population by ...
- 231
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4
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104
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Introduce errors in reference transcripts according to external dataset error model
I would like to modify some reference transcripts from Ensembl (D. melanogaster) to introduce a controlled rate of random errors in the sequences. The idea would be to introduce random base ...
- 2,676
7
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1
answer
733
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How to simulate "base error rate" in art_illumina?
I'd like to simulate 10% sequencing error using art_illumina. The simulator doesn't have a parameter that I can just give the 10%, but it has this:
...
- 2,739
4
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2
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272
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After artificially creating events in a FASTA file, how do I keep track of the old coordinates?
I'm beginning with the reference genome in FASTA format, hg19. I am reading the sequence into a Python dictionary with BioPython:
...
- 1,681
15
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10
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3k
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How to simulate NGS reads, controlling sequence coverage?
I have a FASTA file with 100+ sequences like this:
>Sequence1
GTGCCTATTGCTACTAAAA ...
>Sequence2
GCAATGCAAGGAAGTGATGGCGGAAATAGCGTTA
......
I also have a ...
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