Questions tagged [genome]

for questions related to whole genome analyses. For questions related to individual genes, use tag gene instead. Questions specific to format (like fasta) should be tagged with a format-specific tag.

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Organelle genome genes

How can I get all proteins coded by mitochondrial genome or plastid genome from UniProt. I see UniProt has multiple filtering and search parameters but I could not distinguish between proteins/genes ...
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How to Find List of Genomic Coordinates from List of Genes using UCSC Website?

Suppose I have a list of genes and I want to find their genomic coordinates. To be specific and to keep things consistent with the rest of my project, I'm using hg38 on the website genome.ucsc.edu. So ...
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Why does the SARS-Cov2 genome has letter t

ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC TTTCGAT... is genome of an RNA virus SARS-Cov-2. RNA contains letters C+...
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Create BED file from list with gene symbols

Is there a way to generate a BED file of a list of gene symbols for a given genome?
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Where to find rat genome for STAR alignment?

I'm trying to find the rat genome to carry out STAR alignment for several FASTQ files. Where would I find these files?
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How to know if the DNA sequence has been assembled and why is it important to know how it was assembled?

I have downloaded my FASTA format files, that have the DNA sequences of the coding region of the genes and the DNA sequence of the complete genome, from NCBI. How can I recognize if these sequences ...
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114 views

Converting Fastq files to Fasta files on Ubuntu

I am new to bioinformatics and programming. I tried to convert my fastq files to fasta file, but got this. What could be wrong? ...
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How to quantifiy of specific genes from shotgun metagenome?

I have googled a "lot", couldn't find any specific answer to the question. So, I am here seeking for your guidance. My question is similar to this. I have several metagenome (n=30). But for ...
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Search for specific sequence in group of bacterial genomes

I have a group of L. plantarum genomes. I identified the pangenome using Roary. From the pangenome, I was able to identify unique 'genes' for some of the strains. One of these (actually several were, ...
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Comparing the genetic similarity of human genome and mice/monkey genome - where can I find a list of genes?

I am trying to start a side project where I verify the claim that human and mice/monkey share 99% of their genes. I hope to learn the basics of doing genomic analysis. I would like guidance about ...
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How to identify the DNA sequence of a gene in the complete genome sequence FASTA format file?

I need to identify the sequence of a gene in the complete genome sequence . I thought it was simple, instead it is not a straightforward task ! My method was the following: I downloaded the FASTA ...
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What is the file .mums created by mummer?

I am doing genome sequence alignment using MUMmer, in particular I want to do a dotplot with mummerplot. So the passages that I did are: 1.create a file .mums with the following command line: ...
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STAR aligner multiple fastq files

I’m using STAR to align fastq files from SMART-seq2. I have raw data folder containing sub-folders with samples names the sub-folders each contain fastq file. How can I make a bash command in order ...
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Do RepeatModeler results contain functional domains?

The repeat families predicted by RepeatModeler contain known TEs and unknown ones. How do we know whether some of these may actually be a functional domain of a gene? It's predicted as repeats may ...
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Can we use reference strain as an out-group strain to root SNP based species tree?

I have generated a species tree based on whole-genome SNP using CSI_SNP_Phylogeny, wherein I used Reference strain as an outgroup to root my species tree (SNP fasta were downloaded and RaxML used to ...
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Genome QC + Assembly Pipeline semantics

I’m trying to create a pipeline for genome assembly. How best can I “redirect/pipe” from existing fasta files (or files in general) to other steps of the pipeline? I was thinking of going from the SRA ...
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1answer
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What tools can I use to look up my alleles, genotypes, or phenotypes from my sequenced DNA (WGS)?

(I am not a Bioinformatics expert, please forgive and educate me if I've used any wrong terms or assumptions here) I bought a "Whole Genome Sequence" kit, which gave me the following VCF ...
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Question: Combine BedTools Closest and Window Command

I am new to using Bedtools so please excuse my possible naive question. Let's say my file A is Snps and file B is genes. The Closest command with -k flat let one set how many genes that are closest to ...
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Gold standard benchmark

This page is claimed to contain a gold standard benchmark for viral genome assembly. https://github.com/cbg-ethz/5-virus-mix The claim is here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411778/ &...
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How to filter a genome assembly consistsing of a large number of contigs?

I did some de novo genome assemblies with Illumina PE data using SPAdes, whereas most of them consisting of a large number of contigs(>1000). I have several questions below. Do we need to filter ...
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How to extract certain genes including non-coding regions?

I would like to look at the non-coding regions of some genes. I have around 1000 full genome assemblies and I was able to extract the nucleotide sequences for certain proteins with ...
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1answer
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Mapping protein refseq to Gene ID

I have a protein refseq (eg, NP_000029). How can I get the corresponding gene ID (ag, APC) from NCBI using an R package?
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1answer
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how to train a gene dataset with a nearest shrunken centroid classifier?

I have a data file named "geneexp.csv". the data contains information about gene expression of three different cell types (CD4 and CD8, CD19) I want to classify cells by performing the ...
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Is it possible to filter contaminated reads for raw PacBio sequences (not HiFi reads) before assembly?

De novo genome assembly for non-model organisms face the issue of bacterial contamination. For assembled contigs with mostly bacterial-like sequences (based on BLAST search), the entire contig can be ...
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Merging several fq.gz files or R1 and R2 classes into a single one

I have the following files: ...
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2answers
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How can I subset WGS data to the level of WES variants?

I would like to compare mutational signatures1 in patients from different studies, however some studies are based on exome seq (i.e. ~20,000 coding variants) and some are from whole genome seq (i.e. ~...
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Is it possible to convert BAM file from one genome assembly to the other?

I Have multiple BAM files that are referenced to UCSC genome assembly GRCh37/hg19 that are read in different time frames. Now, I am planning a different studies that require assembling all the data ...
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259 views

kraken2 to OTU table creation

I did run kraken2 and I get two kinds of output How do I generate OTU table from these outputs for phyloseq usage?
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How to fix "expired or not present file ~/.gm_key!" error in braker?

I'm trying to run a braker with genome file only to see if it's working or not before running with all the datasets. But I'm getting this error again and again. ...
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Why does Coronavirus genome contain poly A region at the 3' end in GenBank? [duplicate]

If you look at the Coronavirus genome below, it contains poly-A region at the end. I know that the viral RNA contains a poly-A tail. But, the genome in GenBank is stored in cDNA format. That means the ...
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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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How do I download the mitochondrial haplogroup datasets for human genetics online?

I seem to have landed on the mitomap.org site, but I don't know what to make of it or what do with it / how to get the genomes onto my computer. It sounds like the genomes are stored in GenBank, but ...
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295 views

How to fix RepeatMasker.lib.nsq missing error when running RepeatModelor?

I have run RepeatModelor and I don't see the classified output file. I got this error. ...
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1answer
70 views

Truble to run a multiprocessing kmer count script

Hi there I have this code: ...
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2answers
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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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Resources to learn genome assembly workflow for small genomes (like viruses)

I have sequencing data of a few samples of a DNA genome virus. I'd like to learn de novo assembly of the ...
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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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1answer
2k views

Samtools Index: Chromosome Blocks not Continuous

I am working with short-read whole-genome sequences from the NCBI's SRA. I have aligned and sorted all of my short-read sequences and am attempting to index each sequence into .bai format using ...
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1answer
103 views

Seurat DE t.test

I am new to the Seurat package and was looking at the tutorials on the Seurat website and am just curious to know if there is any way to perform a t.test for the expression of a specific gene between ...
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Coding vs non-coding DNA length

I am trying to calculate the total exonic length (in bp) in order to see where the coding-noncoding ratio of roughly 1% to 99% comes from. We know all chromosomes total about 3 billion base pairs. So ...
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What is the origin of the 'source Gene ID' references given in the 'gene_presence_absence.csv' output of Roary?

I am learning to use Roary for preparing a pan genome for some lactobacillus strains. In the 'gene_presence_absence.csv' output of Roary (which I view in excel), a 'source Gene ID' is given for each ...
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1answer
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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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1answer
56 views

How to use the DI-tector software for defective genomes analysis?

I am trying to use a free .py script from this site http://www.di-tector.cyame.eu/ while unfortunately there's neither manual nor any documentation presented. ...
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1answer
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How can I convert codon coordinates to genomic position?

I am looking for a given mutation in IGV, which accepts coordinates in the form of chr<X>:<Y> Where X is the chromosome number and Y is the base ...
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1answer
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Get a single number representing the contact probability between a pair of genomic loci using HiC data

Hello to the experts in analyzing chromosome structure data in HiC format, I have a very basic question. I have a HiC file (specifics are mentioned below), using which I would like to obtain contact ...
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What does it mean if aligned genomes are not of the same length?

I am aligning 4 genomes of Psuedomonas chlororaphis using progressive mauve software. Command used: ...
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2answers
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how to use list of gene id to get cds sequence(cds fasta file have many annotation, only gene id: is same to query id)

i have a question when i want to extract cds sequence using gene id. but cds file is not just start with >gene is, it has many other annotation. the only same is star with gene: cds fasta: ...
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BERT Language Model and Gene Sequences - How Do I Relate Clusters of Sequences?

I hope you'll indulge a question from a computer scientist with limited bioinformatics knowledge. I've been working with the Google tool for language modeling called BERT. It's generally regarded ...
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1answer
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How can I find the position of every mutation where the Allele Frequency is greater than X, in regards to a reference such as Hg19?

I have a Human genome sequenced in a BAM file (along with other files with the indels, snps, cnvs). I want to find every mutation with regards to the reference Human genome. However the majority of "...
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Getting sequences of one transcript per gene out of annotation and genome

I got a genome (data/genome/genome.fasta) and braker-based genome annotation (data/genome/annotation.gff3), now I would like to ...