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Questions tagged [human]

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2answers
129 views

How to cluster the human genes by pathways/system-biology/metabolic properties?

I would like to make a chord plot from my data. I have a list of genes that according to my experiments are divided into 64 clusters of enrichment pattern. I would combine my 64 clusters with a ...
3
votes
1answer
34 views

Seeking explanation of the hg38 files downloaded from bowtie 2 website

I downloaded the H. sapiens, NCBI GRCh38 files from Bowtie's website. After unzipping, there are 6 files, 4 that end in set 1.ebwt, set2.ebwt, set3.ebwt, and set4.ebwt and two that end in set.rev.1....
1
vote
1answer
29 views

List of human transcription factors

I'm looking for a list of human transcription factor (TF) genes. Where can I find a TF database or how can I retrieve this list from other databases?
2
votes
1answer
38 views

remaining human genome variation that hasn't been sequenced?

Given all the genome variation information we have accumulated from resequencing human genomes up until now (early 2018), how much variation is left that hasn't been sequenced? EDIT: given one of the ...
2
votes
1answer
81 views

How to retrieve SNPs data of different humans?

How can I retrieve only SNPs from the dbSNP's FTP site. The files are gzipped and organized by human chromosome (i.e, chr[1-22,X,Y]), are these for one human? I need only SNPs data for various humans.
7
votes
1answer
270 views

ethnicity check either from bam or vcf files

What tool could I use to check the ethnicity of a human bam or vcf file? I would like to use the results as a QC check to know whether a given sample or set of samples match the ethnicity information ...
4
votes
1answer
33 views

Finding data to validate results

My group has a complex datset and I would like to validate the results and check the methods I use in a similar dataset (better if it has been already studied). Characteristics of my dataset: It is ...
7
votes
1answer
170 views

What's a good ontology for drug names?

I have ... A database with patient phenotypes in, stored as HPO terms Genetic data in whatever format I need I want ... To store drug names in a way that won't make my life difficult If it's ...
3
votes
1answer
188 views

genes with highest RPKM/FPKM for a human RNA-seq experiment?

Which genes/transcripts show up as having the highest RPKM/FPKM on a human RNA-seq experiment? Is it usually the same genes/transcripts? EDIT: mRNAs (e.g. poly-A RNA-seq preps) and not including ...
4
votes
3answers
176 views

what percentage of the human genome is MAPQ=0?

When doing Illumina 2x150bp sequencing of genomic DNA, and after aligning the reads to GRCh38, what percentage of the non-N fraction of the human genome is MAPQ=0? This is, what part corresponds to ...