Questions tagged [validation]

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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....
Shafayet Rahat's user avatar
2 votes
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INDELS in PLINK files converted to VCF

I want to compare/validate variants called from sequencing data with array (plink format) variant data. I converted the plink files (.bim, .bed, and .fam files) with plink1 to vcf files. ...
Dandelion's user avatar
  • 303
2 votes
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Where can I visualize Ramachandran plot?

I am using Rampage webserver to obtain a Ramachandran plot. However, the server does not reveal any plot just values (favored, allowed, outlier regions). Can you recommend other similar web sites?
polonio210's user avatar
3 votes
2 answers

Difference between clinical significance and statistical significance

I am working on a clinical data analysis project and am from IT domain. While I am analyzing the data, I came to know that though some of the variables are not statistically significant, they are ...
The Great's user avatar
  • 227
2 votes
1 answer

Metagenomic shotgun data with internal control

For 24 human stool samples I have metagenomic shotgun reads from an Illumina platform. The reads were filtered and mapped against a bacterial species library and specific maps to species were kept and ...
Rene's user avatar
  • 21
6 votes
1 answer

How to validate that BAMs have been downloaded correctly?

I currently have several hundred BAM files which were downloaded by someone else. These have remained untouched---before working with them, I would like to double-check that these BAMs have been fully ...
EB2127's user avatar
  • 1,413
0 votes
2 answers

Is there a standard method to validate whether a bigWig file is correct?

I have a bigWig file of extension *.bw (which is standard), but I am suspicious that this file may be of an incorrect format. Is there a standard method in the ...
ShanZhengYang's user avatar
6 votes
1 answer

Verify a predicted protein in one genome in a different genome of the same species

I have two genome assemblies of the same non-model species, call them Assembly 1 (generated from Illumina data) and Assembly 2 (generated from PacBio data). For Assembly 1, I also have predicted ...
aechchiki's user avatar
  • 2,676