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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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Are there efficient tools for PANGENOMES visualization (GFA size >2GB)?

I've been looking for a program that allows me to visualize pangenomes efficiently and it has been very difficult find satisfactory documentation about large pangenome's visualization tools since most ...
AIsaac's user avatar
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How to compare CDS, CNE, miRNA, UCNE across new related genomes?

I have 5 sets of raw Illumina whole genome shotgun data from 5 different species, and 3 reference genomes that are assembled/annotated, I want to produce a similar table to Table S2 of this paper: ...
JohnDoe23's user avatar
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1 answer
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Why is mtDNA not labelled as such for many organisms?

Also posted on biostars While I was searching the genomes of some eukariotic organisms (fungi,plants,protists) even though I knew that they had mitochondrial DNA,when I searched their genome structure ...
George X.'s user avatar
3 votes
1 answer
196 views

low mapping percentage in bwa mem

After aligning paired-end reads to a reference genome, I am getting low percentage: ...
Moon's user avatar
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3 votes
2 answers
141 views

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 ...
Moon's user avatar
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1 answer
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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 ...
rimo's user avatar
  • 1,003
1 vote
1 answer
268 views

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 ...
Joonatan's user avatar
3 votes
0 answers
78 views

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 ...
Dandelion's user avatar
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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 ...
BigMistake's user avatar
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1 answer
120 views

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 (...
Umar's user avatar
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3 votes
1 answer
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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 ...
Cristian Riccio's user avatar
1 vote
1 answer
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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 ...
venkatesh war's user avatar
1 vote
1 answer
61 views

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 ...
venkatesh war's user avatar
1 vote
1 answer
558 views

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 ...
Shafayet Rahat's user avatar
2 votes
1 answer
128 views

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: ...
ashenflower's user avatar
4 votes
1 answer
346 views

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. ...
Liam T Sullivan's user avatar
1 vote
1 answer
245 views

file path of BiocManager:install()

I was trying to format my GWAS summary statistics with the MungeSumstats R package and would need to install ...
Lloyd_LiuSiyi's user avatar
1 vote
1 answer
55 views

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 ...
Gerald Vasquez Aleman's user avatar
3 votes
0 answers
617 views

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 ...
rimo's user avatar
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0 votes
1 answer
306 views

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/...
gc5's user avatar
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0 answers
405 views

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. ...
Abhishek Pandey's user avatar
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0 answers
214 views

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, ...
Anik Dutta's user avatar
0 votes
1 answer
71 views

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 ...
Anik Dutta's user avatar
0 votes
1 answer
41 views

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 ...
Smiletree's user avatar
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2 answers
478 views

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 ...
abc's user avatar
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1 vote
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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 ...
art987's user avatar
  • 11
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0 answers
36 views

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 ...
AWE's user avatar
  • 121
2 votes
1 answer
87 views

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 ...
Christa Frodella's user avatar
1 vote
2 answers
86 views

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 ...
Igor's user avatar
  • 111
2 votes
1 answer
159 views

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 ...
0x90's user avatar
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1 vote
1 answer
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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 ...
juanjo75es's user avatar
1 vote
1 answer
184 views

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 ...
juanjo75es's user avatar
1 vote
0 answers
40 views

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 : ...
Eliran Turgeman's user avatar
1 vote
2 answers
208 views

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 ...
Tripoli's user avatar
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0 votes
3 answers
463 views

Get gene sequence based on the annotation

I've got the reference genome with Python like so: ...
CheesyGnocchi's user avatar
1 vote
1 answer
106 views

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 ...
719016's user avatar
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1 vote
0 answers
15 views

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 ...
annabelperry's user avatar
1 vote
1 answer
66 views

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, ...
annabelperry's user avatar
0 votes
2 answers
85 views

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 ...
An Ignorant Wanderer's user avatar
1 vote
1 answer
127 views

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 ...
user345394's user avatar
3 votes
1 answer
70 views

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 ...
Jesse's user avatar
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2 votes
1 answer
52 views

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 ...
LauraR's user avatar
  • 127
3 votes
1 answer
3k views

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 ...
user1995's user avatar
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0 votes
1 answer
186 views

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 ...
terdon's user avatar
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4 votes
1 answer
495 views

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 ...
Konrad Rudolph's user avatar
0 votes
2 answers
574 views

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/...
Zizogolu's user avatar
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5 votes
1 answer
326 views

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 ...
LinuxBlanket's user avatar
2 votes
1 answer
339 views

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 ...
conchoecia's user avatar
  • 3,181
1 vote
1 answer
801 views

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 ...
San's user avatar
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2 votes
3 answers
261 views

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 ...
L R Joshi's user avatar
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