Questions tagged [human-genome]
The human-genome tag has no usage guidance.
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Using CoRAL to reconstruct ecDNA
We are trying to use CoRAL to reconstruct ecDNA. However, we have a problem in CoRAL.py reconstruct, when an error is obtained in infer_breakpoint_graph step. The only difference is reads' article are ...
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Verify cell identity
We want to analyze from an article the sequencing data (3 rd generation) of the U2OS line, and we would like to verify if it is that cell line. I was wondering how would be the general procedure, or ...
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How do I infer sex from a VCF file?
I have human samples VCF files that I want to infer the sex of. I do not have sequencing information or information about coverage. What's the best way to go about this? I'm looking for a robust and ...
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annotate ChIP-Seq peaks
I'm attempting to annotate several peaks with various approximations. Nevertheless, the expected results are not achieved.
T_S_1 is a Granges object which the ...
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Aligners for repetitive sequences
we are interested in detecting repetitive sequences in two cell lines, however, when performing the alignment with pbmm2 on GRCh38, not good results are obtained. We are trying to modify the ...
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Where can I get hg38 Copy number Variation (CNV) file?
I'm wondering how can I get standard hg38 Copy number Variation (CNV) file from UCSC website.
Although, I got a link that is not working: http://hgdownload.cse.ucsc.edu/goldenPath/hg38/encodeDCC/...
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Where to find the homopolymer regions bed file for Hg002 genome?
This question was also asked on Biostars
I am doing an experiment where I am trying to analyze the errors in the homopolymer regions between the polished reference hg002 genome and hifiasm assembly ...
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What is it about gene names starting with "LOC"?
I was struggling to use AnnotationDbi to change my ensemble ID to gene name, for datasets of three different species (human, canine, mouse). Among gene names for all three species there are genes with ...
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How many Ns and ns in GRCh37 / GRCh38 per 'canonical' chromosome?
This is kind of pedantic, but I'm not sure where to look...
For GRCh38 (and a lot of work...) I have the following...
...
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The current status of human genome annotation
I was wondering if you can suggest something on the current status of the human genome annotation efforts. I know about ENSEMBL/HAVANA/GENCODE, and I've read the relevant papers; however, I was ...
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What should GC coverage bias plot of exome data look like?
I want to see if there is any GC coverage bias in some paired-end Illumina human exome data. Update This is for a variant calling project. I used the ...
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How can I assemble my genome from raw files?
I've had my whole genome sequenced (at 30x average coverage) by a lab, and they have provided the raw files to me (BAM, FASTQ, and VCF).
How can I assemble it?
And does assembly provide any further ...
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Recode bgen files against reference genome
I have a set of .bgen files split by chromosomes, including both SNPs and INDELS (named with both rsids and chr_pos_a1_a2). I know a large portion of them are encoded on the wrong strand, and I want ...
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Find the genomic locations of exons of certain human gene
So I know Consensus CDS has the genomic locations of exons, however, only of the exons in the CDS. Everything before or after is not included.
NIH variation viewer has those (kinda-) radio buttons ...
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What does 'Human Alternative sequence Gene' mean in Ensembl?
I have downloaded a dataset containing RNA-Seq RPKM (reads per kilobase per million) values for 52376 genes (in humans). To find RPKM values for the gene KIR2DL2 in the dataset, I have to search for ...
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Synteny test and tools to use for mammalian organisms?
I am trying to do a synteny test for MHC genes in human and another mammalian organism
For this reason, I need to download all paralogs of rabbits from humans and then construct position the ...
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How to compare 2 whole genome sequences [closed]
I have the files of 2 persons that got whole genome sequencing, one by nebula genomics and the other by dante labs.
I want to compare their genomes to see if they are father and son.
I want to see ...
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Question about public availability of human SNP dataset with country of origin
Is there a publicly available data set for humans SNPs, preferably together with the country of origin? If so, could someone please point me towards it.
I've looked through other questions on the site ...
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What tools can I use to look up my alleles, genotypes, or phenotypes from my sequenced DNA (WGS)?
I bought a "Whole Genome Sequence" kit, which gave me the following VCF files (this service did not include any analysis, just the raw data):
cnv.vcf
<...
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Get raw genome sequence
I'm currently working on testing some matching algorithms for strings. I would like to do some tests on raw genomic data as I expect different results from random strings given the lower entropy. How ...
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What are the coordinates of the extended major histocompatibility complex (xMHC) in GRCh38?
Is there an accepted boundary of the extended major histocompatibility complex (xMHC) in human? Specifically, I am interested in the boundary coordinates for Genome Reference Consortium Human Build 38 ...
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Power calculation for GWAS/EWAS
I want to investigate, how much sample size i needed to obtain 80% power for GWAS/EWAS studies. Phynotype trait is discrete (not case/control) for human disease.
I wonder, does anyone has came across ...
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Download or create VCF from Human Genome Diversity Project (HGDP)
I can't seem to find HGDP data in VCF format.
Does anyone know where I can download it from?
Perhaps there a Snakemake pipeline for calling VCFs from this data?
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Difference between "trans-ethnic" and "cross-ancestry"
A quick terminology question today. I see the terms "cross-ancestry" and "trans-ethnic" used seemingly interchangeably in literature. Is there any real difference between those two ...
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List of global ethnicities
Looking at the 1000 genomes project I see the following list of population groups and super-groups:
https://www.internationalgenome.org/category/population/
However, is there something like a ...
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How can I bypass 'out of memory' problem using a HISAT2 for human genome indexing?
I am trying to perform a HISAT2 indexing using a GCF_000001405.39_GRCh38.p13_genomic.gtf and ...
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A .gtf file for HG38 for HISAT2 indexing
I am trying to build a HISAT2 index using Pertea et al. procedure (https://www.ncbi.nlm.nih.gov/pubmed/27560171) using their extract_splice_sites.py and ...
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Theoretical limit of human genome compression
How small can a compressed file containing the human genome be?
I'm aware that this question cannot actually be answered, since it is asking for the Kolmogorov complexity of the human genome, which is ...
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Compressing the human genome to few megabytes
Multiple sources (see for instance this or this) discuss how genetic data will have scalability problems, given the huge file size of the human genome. The most straightforward encoding (see here) of ...
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Detection of CNV(InDel) of intermediate size
My impression is that small InDel (a couple of bp) is identified through cigar string in BAM and typical CNV (at least thousands of bp) is detected through read depth.
What about InDel or CNV with ...
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Obtaining HGDP project data in fasta format
I need to obtain sample data from modern humans in fasta format. I just need some megabytes of data from every individual. I actually use a script that obtains the cram file from here (ftp.1000genomes....
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Authoritative source on human cytogenetic regions?
I am looking for a database that would keep track of human cytogenetic regions and genomic coordinates per genome assembly. I had expected the Genome Reference Consortium to have it, or Ensembl, or ...
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Reproducing population structure from 1000 Genomes Data
I recently tried to reproduce population structure with 1000 Genomes Project data (Phase 3, 2504 people).
According to supplementary material,
To reduce the dataset, we used VCFtools to only keep ...
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Meaning of the FORMAT fields of the VCF file coming from GIAB project
After reading the GIAB paper in https://www.biorxiv.org/content/early/2018/05/25/281006 and its Figure 1, I am still having trouble understanding the data inside the GIAB VCF file for HG001 (...
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Public access to genomics databases
I'm a statistician, and am interested in applying the theory of algebraic Markov models to genomics. Here's one paper I'm interested in: Large-scale genome-wide association analysis of bipolar ...
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Does the DNA or RNA of some ethnic groups map better than others' to the human reference genome sequence?
I believe that the human genome reference took DNA samples from different people and that some natural variation is included in extra contigs.
However, the human reference genome comes from a ...
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Least present k-mers in the human genome
What are the least present k-mers in the human genome at different sizes?
Starting with k=4 and going up in size until k=10, what are the k-mers least seen (or not at all) in the human genome? I am ...
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Dealing with indels when converting a position to chromStart and chromEnd for a bed file
Starting with a chromosome # and position, I am trying to get chromStart and chromEnd values for a .bed file, but I am not sure how to calculate chromEnd when I have a variant that is an insertion or ...
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TCGA bam file duplicates (aligned reads) and related last part of TCGA barcode
I am running an analysis on TCGA bam files (GCRh37/hg19) of whole exome sequencing data.
I usually find one bam file for each sample. However, at least one sample has two bam files, in which the last ...
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hg38 GTF file with RefSeq annotations
I'm not sure what I'm missing, but I'm struggling to find an official hg38 GTF file with RefSeq annotations. I'd like to provide ...
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Retrieving a list of human genes having GO associations
I need a command in R to retrieve all human genes associated with a Gene Ontology entry. I tried to look for it online but did not find it.
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Using BLAT command line tool to blat split sequences
I have the nucleotide sequence:
AATTGAGGCACATTTTTTTTTAGACAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGTGTGATCATAGCTCACTGCAGCCTCGACCTCCTGGGCTCAACAAAGCACACAGTGGGCGGATCCCCACCAG
When I blat this on UCSC Genome ...
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What is the standard way to work with a diploid reference genome? Complementary strands?
At the moment, the standard reference genomes (e.g. hg19, hg38) are haploid genomes. We know that the human genome is diploid. Naturally, the latter would be the respectively correct representation of ...
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Dataset: Locations of regulatory sequences in the human genome?
I am looking for the positions of annotated regulatory sequences (promoters, enhancers and suppressors) in the human genome.
I looked at Ensembl regulatory Build and PAZAR but I am not used to look ...
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How do I generate a variant list (i.e. VCF file) using Illumina reads from a human genome?
This is a problem I have to solve frequently, and I'd be interested in knowing what other methods people use to solve the same problem.
About twice a year, I get asked to determine variants from ...
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Can a customized GRCh38 .gtf file be used with any of the GRCh38 released patches?
I got a customized GRCh38.79 .gtf file (modified to have no MT genes) and I need to create a reference genome out of it (for 10xGenomics CellRanger pipeline). I suspect that the .79 part is the ...
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State of the art in predicting Translation Initiation Sites
I'm working on a university project of predicting Translation Initiation Sites in human DNA. I searched the net for papers and documentation to get guidelines and inspiration, but I feel uncertain ...
user548
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Downloading a reference Genome for Bowtie2
How do I download a reference genome that I can use with bowtie2? Specifically HG19. On UCSC there are a lot of file options.
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Working with old genome builds
Is working with and relying on old genome builds still valid?
For example NCBI36/hg18. Would results from papers based on old builds require LiftOver and re-analysis to be useful?
A bit of context, ...
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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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