Questions tagged [reference-genome]
A reference genome (also known as a reference assembly) is a digital nucleic acid sequence database, assembled by experts as a representative example of a species' set of genes.
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low mapping percentage in bwa mem
After aligning paired-end reads to a reference genome, I am getting low percentage:
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Reference genome (bwa -mem)
I want to do mapping with bwa mem. I downloaded a reference genome from ncbi database which is (Danaus plexippus). I got one ncbi_database.zip file which contain 2 ...
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Constructing a pangenome graph using multiple samples
I am working with yeast strains (specifically S. cerevisiae) that have been cultured and evolved over many generations in the lab. I am using the reference S288C strain when I do certain analyses but ...
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LD clump GRCh38 GWAS results
The vignette of R package ieugwasr describes a plink based wrapper function for LD clumping GWAS data using the 1000 genomes ...
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Different human reference genomes from NCBI and ENSEMBL, and variant annotation with Variant Effect Predictor (VEP)
Background: I have been working on a human variant calling pipeline, from whole exome reads to variant annotation.
For variant annotation I used the Variant Effect predictor (VEP), which is Ensembl ...
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Is a human genome file with reference as NCBI37 the same as hg19?
This question was also asked on Biostars
In other words, are NCBI37 and hg19 synonymous? I can't find much information for what NCBI37 is in a human (not mouse) genome.
The VCF is from a lab ...
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Calculating total number of Unique gene in every genome from ROARY pangenome output
I performed a ROARY from 100 genome. I got several file including gene_presence_absence.csv from the results. I want to know how many unique gene(unshared gene, based on blast homology, same gene (...
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Which human reference genome version does VARAdb use?
I am interested in annotating a list of variants using VARAdb. My coordinates use the GRCh38 (hg19) reference genome. However, I do not know which coordinate system VARAdb uses.
A section of the ...
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How to get a file with the introns of a gene?
I was able to get the exons of a particular gene as a fasta file from the NCBI genome viewer. As for introns I only found a bed file that showed where the intron starts and ends, along with its ...
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How to subset an SRA file for a single chromosome?
I used prefetch to get the Pacbio reads of chicken from the SRA database. I want to align these reads against a reference genome, but not all the reads. I am only interested in a particular region on ...
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split fast reference fast file by 22 chromosome
HG38 human reference is the collection of reference from all 22 chromosomes,x,y chromosomes, and some others. I was targeting to split the reference file into 22 chromosomes fasta files. I am ...
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CNVKit does not output all the accessible regions in the targets bed file
This question was also asked on Biostars
I am using CNVkit on my data using hg38 as reference. The command that I am using is the following:
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Breseq error (code 137). Any ideas?
The code I ran was here, so nothing fancy.
breseq -l 110 -o RifR_align -r Big_burk_assembly.fasta RifRNano_nanopore.fastq.gz
This was the output.
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file path of BiocManager:install()
I was trying to format my GWAS summary statistics with the MungeSumstats R package and would need to install ...
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How to identify mutations in a viral genome
I have a fasta file with multiple sequences comprising 38 sequences. The length of the sequences are around 11000 bp.
How can i get changes in the genomes based in a reference genome? (aa subtitutions ...
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Aligning PacBio HiFi reads to reference genome using pbmm2
I am trying to align a yeast strain sequenced by PacBio HiFi reads to the reference genome S288C (https://www.ncbi.nlm.nih.gov/data-hub/genome/GCF_000146045.2/) using pbmm2 but for some reason I am ...
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Extract chromosome arms' coordinates for specific reference
I would like to get chromosome arms' coordinates for genome reference hs37d5 (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/...
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How to combine multiple .fasta files of primary assembly from Ensembl into one for sequence alignment?
I have some marmoset snRNA reads that I want to align with the reference transcriptome using cellranger. The primary assembly for marmoset is available here, which is broken down into 22 parts. ...
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How to manually curate a genome assembly for sequence variation or error?
I have a PacBio HiFi assembly of 1.1 Gb from a heterozygous species. I have aligned this assembly against a reference genome which is around 0.9 Gb. I can see that there are quite a few INDELs, ...
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How to improve a genome assembly using Dovetail and PacBio assembly?
I have more of a conceptual question. I have two genome assemblies from the same plant, one from Dovetail technology (~998 Gb) and another is PacBio HiFi assembly (~1.1 Gb). The Dovetail assembly is ...
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how can I get expression of an inserted foreign genes?
hi we have transgenic mice with human gene inserted. if we profom rnaseq for the mice, how can we get the expression value of the human gene inserted to the mice? and use this expression to compare ...
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How to compare sequences of genes obtained after whole-genome sequencing to reference genome?
My idea is to align whole-genome sequencing data (as fastq files after, 30× coverage, gDNA) to the reference mouse genome (NCBI), extract the immunoglobulin locus and compare it to the reference. I ...
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What is the 4th "level" of version number for the S. cerevisiae reference genome?
yeastgenome.org has releases called R64-1-1, R64-2-1, etc, with 3 "levels" of versioning but in a few places I have seen a "fourth level". For example, Ensemble calls their hosted ...
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Fastest way to count where two bam files are homozygote reference (inverted variant calling)
Maybe I'm having a brain-freeze so excuse me if this is a waste of everyone's time...
I am working with an organism with ~700Mb genome.
I have bam files of two individuals that are whole genome ...
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Splice variant analysis with ensembl genome/annotation/rna. Which files do I use?
I am running splice variant analysis. I wanted to use NCBI genome but the program works better with ensembl. I am a bit confused on primary vs. top level to use as my reference genome. I also do not ...
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Solutions to reference bias issue
I've recently learned about the reference bias issue - inability to properly map NGS reads in certain genomic regions caused by the fact that our standard genomic references are linear and do not ...
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Are there open-sourced graph-based variant callers?
I would like to compare GATK with graph-based variant callers. I have seen the Fast and accurate genomic analyses using genome graphs paper from SevenBridges and the paragraph tool by Illumina, though ...
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Which one is a more convenient assembly?
I have developed a software for de novo genome assembly. Its performance varies gradually according to how much data you employ. At initial stages it often produces contigs that look like that when ...
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Interpreting contig alignments to a reference genome
I have applied two de novo genome assembly tools to data from the run SRR12707453, corresponding to a phage (I downloaded the data and have no relation with the authors of the study).
Using rnaSPAdes ...
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Filtering pileup from site lists
I want to write a script that filters a pileup file from a site lists file.
As an input I get a reference genome, pileup and site lists files.
Example of an output for this script:
Pileup File :
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How can I get or create a reference genome for Bacteria?
I am a computer engineer and nowadays trying to grasp some concepts of Bioinformatics particularly, reference genomes and genomic variants. My aim is to find the effect of sequence features on variant ...
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Get gene sequence based on the annotation
I've got the reference genome with Python like so:
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Gap-fill assembly with PacBio reads
I would like to gap-fill (or correct) a mammalian-sized assembly for which we have BACs that have been sequenced with PacBio CLR data. I have seen there are pbm22/gcpp tools available for correcting ...
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How do I include repeat purity, default slippage, default stutter, and minimum flanking (left and right) in Tandem Repeat Finder's output?
I am attempting to create a markerInfoFile for use in a program called popSTR (GitHub Documentation: https://github.com/DecodeGenetics/popSTR). The marker info file should contain information about ...
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BWA: Detecting Variation between Reference Genome and Short-Read Sequences
I need to identify all loci in the short-read sequence at which the number of microsatellite repeats (i.e. number of copies of "AA," "GTC," etc.) differ from the reference genome, ...
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Clarification about how mapping to a reference genome works in RNA seq
When mapping reads to a reference genome, how is it possible to tell which part of the genome the read is referencing if the genome possibly has the same repeated sequences in different areas? What I ...
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How to identify the reference genome assembly used to create a .hic file?
I have a bunch of .hic files of different species. But, I don't know which reference genome assembly (e.g. GRCh37 or GRCh38 in the case of human genome) the genomic co-ordinates of the .hic file ...
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Why do these NCBI representative genomes for ape species have no Y chromosome?
I recently downloaded a genome from NCBI for chimpanzee and was surprised to see no Y chromosome. I added in one from a separate accession and carried on, but then today went to do the same for ...
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How do researchers account for heterozygosity in genome assembly?
this is a very general question about diploid genome assembly. I am wondering how people deal with heterozygous region in a genome when assembling ?
Do they pick one of the haplotype to be in the ...
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How to find novel transcripts using GFFcompare?
I am trying to find novel transcripts from an RNA-seq database. Based on the advice I got, it seemed that using Stringtie for transcript assembly is a good way to go, and it supports novel transcript ...
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How should I deal with segmental duplications when aligning NGS reads to a reference genome?
This is a follow-up of my other question. I have been having trouble calling variants in the human SMN1 and SMN2 genes, because the human genome has a large segmental duplication there and these two ...
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Old versions of the reference genome and dbSNP
For benchmark purposes I’m trying to find an old version of the human reference genome (pre-GRCh37) and a matching version of dbSNP.
Unfortunately it appears as though older versions of dbSNP aren’t ...
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Downloading Fasta for each chromosome of a complete genome
Whatever I am googling I am not able to find fasta file of each chromosome for hs37d5.fa. hs37d5.fa whole fasta file however is here
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/...
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At what stage of a transcriptome assembly is it better to perform read contaminant filter?
I'm trying to assemble a bivalve transcriptome. Since bivalves are filter feeders, their transcriptomes tend to be highly contaminated by bacteria, algae and whatnot. Since I pooled several ...
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How to force pilon to correct a reference with low coverage mapped reads?
I have mapped some reads to a reference and want to change SNPs in the reference to SNPs found in the reads, even at low coverage. For example, here is a screenshot of one reference in IGV that I ...
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STAR Indexing Diference for Small and Large Genome File Output
I have a quick doubt on the output of the Genome Indexing, I have used the STAR program along with genome .fasta file and GFF file.
Genome size is 3GB, here is the file output
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Genome scaffolding
I have assembled a virus genome using Ray resulting in approximately 5000 contigs. Now I want to build a scaffold of those contigs to get the full genome (I am aware of the fact that there might be ...
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GRCm37-designed exon target enrichment, which reference to use?
I have exomes from 24 individual mice. The exomes are the product of Roche's SeqCap EZ HyperCap target enrichment kit. I see that the mouse exome design comes from mm9/NCBI37, the previous major ...
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What process and input data is required for a cellranger reference transcriptome?
I'm analysing single-cell RNA-Seq data using the 10X Genomics cellranger platform. While they provide reference data for Mouse and Humans, other species require a ...
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Number of reference sequences in a SAM file
From a single record, I can get the reference sequence ID from the field rID, but how can I get the total number of different reference sequences stored in the whole SAM file?
It can be simple as just ...
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