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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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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Comparing loci across catalogs

Context: I'm using the Stacks (v2.59) ref_map.pl command to analyze garden and wild samples of a plant species, and have aligned my paired-end RAD reads to a reference genome (using GSNAP). The goal ...
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Cross-checking metagenomics analysis via reference genomes

I'm looking at verifying metagenomic pipeline output for small genomes (viruses) on short read data. Background Most of the work in small-genome metagenomics is performed using bacteria and I'm ...
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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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Does the galGal5 chicken assembly have a chromosome 29?

The chromosome sizes at UCSC don't seem to contain chr29: ftp://hgdownload.soe.ucsc.edu/goldenPath/galGal5/bigZips/galGal5.chrom.sizes It has a chr28 and a chr30. Am I missing something or is there ...
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How to get results from Homo.sapiens package in bioconductor for a specific reference

I want to use the Homo.sapiens package in Bioconductor to retrieve the chromosome location start and end for each gene symbol in a specific reference (e.g. hg19 or hg38). Right now, I am using the ...
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4 votes
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Two variants associated with same chromosomal position in genotype data for one individual

I'm trying to play around with my family's raw genetic data from Ancestry.com so that I can do some genetic analyses, and I noticed in the AncestryDNA raw data files that some regions of the genome ...
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How can I subset a reference based on only the first chromosome?

I have the GATK FASTA reference for hg19. I would like to subset this based on the first chromosome. Normally what I do is open the FASTA as a text file, and then delete all other chromosomes except ...
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population admixture

I am new to Admixture and I would like to use fastNGSadmix to look for admixture in one individual (modern). Admixture is supposed to look for proportions of ancestral populations in a sample (either ...
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Java error when launching Pilon

I am trying to use Pilon to improve a reference based on some Illumina data I have got. So, I aligned the Illumina reads to the reference using bwa. Then, I want to use Pilon to improve the reference ...
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5 votes
2 answers
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Creating a new reference genome B by changing genome A with mismatches from BAM file without long reads

This question is slightly related to this one: Improve a reference genome with sequencing data Only in my case, I have a starting genome reference A, of a short phage genome, and reads from a related ...
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6 votes
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Bacterial genome annotation of a clinical isolate strain?

So I'm basically so new to this that I'm just trying to find out what tools, methods, and keywords I should go look up by myself. I have a unique strain of a bacteria. I was given RNAseq data for ...
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Is it possible to do alignment within Python? Check variants against reference?

I'm currently adding a few SNPs randomly into a FASTA within python using BioPython. In the following example from BioPython, I add an SNV at location "5" http://biopython.org/DIST/docs/api/Bio.Seq....
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Given a Genomic Ranges of SNPs, how to inject these SNPs in genome via BSGenome?

Let's say I have the genome hg19 loaded into R via BSGenome ...
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4 answers
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How to manipulate a reference FASTA or bam to include variants from a VCF?

I have some software which takes fastas as the input. I need to include SNVs and InDels from a VCF into the reference hg38 and then use this. The problem is, I don't know of an algorithmically sound ...
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2 votes
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Is there a way to retrieve ENSEMBL IDs from a search query?

I would like to be able to batch download FASTA files from ENSEMBL. I normally would use the API to download them from the ENSEMBL gene IDs. However, the IDs aren't ones I know, only ones I would get ...
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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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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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