Questions tagged [data-management]

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28 views

Blood analysis devices: how and where is the data saved

I've read that there are blood analysis devices that can automatically determine the data for each specified analyse. You can expect to get the results in less than a day. Q: How and where do they ...
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36 views

How could I find Differential Genes in Expression Matrix File by R?

I tried to get gset of my dataset by getGEO function, but unfortunately it didn't work( I installed GEOquery package) and i get errors like this: Found 1 file(s) GSE69606_series_matrix.txt.gz trying ...
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41 views

How to compare multiple genetic profiles in Python?

I have hundreds of vcf file where each vcf file contains genome profile for a tissue. A portion of the vcf file is as follows: [ I can read each vcf file into a dataframe. So it would be hundreds of ...
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3answers
64 views

Getting a stretch of genomic ranges from a dataframe/granges object based on metadata column

I have a "test" data.frame object in R, which is basically a small subset of a 66000 row dataframe, which looks as follows: ...
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2answers
240 views

How to merge .fastq.qz files into a single .fastq.gz with their same id without losing any content in parallel

I have a large number of .fastq.gz files of different lane and reads. I have to merge them each reads group files into single .fastq.gz files. **eg: 1st type NA24694_GCCAAT_L001_R1_001.fastq.gz ...
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1answer
112 views

how do I convert a vcf file for a GWAS study (using R package vcfR)

I have a vcf file with individual level genetic data, that I read using the R package vcfR ...
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2answers
59 views

Calculate average parental genotype

I am interested in creating an averaged value for genotype across two parents: E.g. Input (three unrelated couples, 1, 2 and 3): ...
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0answers
26 views

Does anyone have older versions of NT and 16s RNA DB from NCBI?

I am in search of past years' versions of NT and 16s databases from NCBI. I recently contacted NCBI about this and they replied: Unfortunately, we do not archive past versions of the blast ...
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31 views

Why is Clostridium difficile toxin A + B outdated in snomed?

I'm looking at the new version of the Snomed dictionary and the concept 707993000 Clostridium difficile toxin A + B (substance) is deactivated (and outdated) since ...
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1answer
45 views

Impute phenotype under some constraints

Errors happen frequently in the lab and I got one sample that we mixed one important information (the region of the sample) between two samples. Now we don't know which sample is from which region, ...
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3answers
564 views

How to split multifasta based on partial fasta header

I have download a batch of refseq fasta files and want to split them based on strain. this is complicated by accession numbers, project IDs etc. I downloaded the genomes via eDirect from NCBI. I know ...
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2answers
135 views

Solutions for managing data in a small bioinformatics / 'omics lab?

A different sort of problem: even a small 'omics lab generates a lot of data, raw, intermediate and processed. What (software) solutions exist for managing this data, such that "old" data can be ...
2
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1answer
50 views

Is Wikidata a reliable KB for genomic and drugs annotations?

I'm looking for a Linked Open Data approach to annotate a dataset with human genome and drugs information. According to the Linked Open Data cloud, there are a lot of interconnected ...
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1answer
328 views

The state, limitations and comparisons of large variant stores

Background: We're increasingly needing some way of storing lots of variant data associated with lots of subjects: think clinical trials and hospital patients, looking for disease-causing or relevant ...
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7answers
571 views

How to version the code and the data during the analysis?

I am currently looking for a system which will allow me to version both the code and the data in my research. I think my way of analyzing data is not uncommon, and this will be useful for many people ...