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.

26 questions with no upvoted or accepted answers
Filter by
Sorted by
Tagged with
4
votes
0answers
73 views

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: ...
3
votes
0answers
1k views

How to install DnaSP on a Mac

I need to install DnaSp, but its not working on my mac. I'm using wine to install it using these instructions for wine. it successfully installs but then I get this error ...
2
votes
0answers
22 views

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 ...
2
votes
0answers
28 views

What Cellbase resources are 0-indexed, and which are 1-indexed?

The UCSC Genome Browser Team is clear about that the genome browser GUI indexing which is 1-based, closed interval. Genomic sequence retrieval via the UCSC REST API is 1-based, closed interval. All ...
2
votes
0answers
24 views

Do additional peaks in percent GC of PacBio gDNA reads indicate contamination?

I have two sets of PacBio reads from genomic DNA of an Aspergillus species that were made from separate preps of the culture. One of them has two additional peaks at 38% and 60% in the percent GC ...
2
votes
1answer
114 views

How to visualize genome track of gene in specific cell-lines?

I'm trying to make a plot showing genome tracks of specific genes in specific cell-lines of RNA-seq and Chip-seq data. It should look something like this I have recently seen this encode, but in ...
2
votes
1answer
70 views

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 ...
1
vote
0answers
30 views

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 ...
1
vote
0answers
56 views

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 ...
1
vote
1answer
45 views

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 ...
1
vote
0answers
11 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 ...
1
vote
0answers
35 views

Is it possible to determine the genomic context of a gene in a Whole Genome Shotgun project?

I performed several BLAST searches and identified several genes of interest in a Whole Genome Shotgun (wgs) project. I know that gene X is located on scaffold 1234, from nucleotide 1 - 2250, while ...
1
vote
0answers
16 views

Finding gene name from human genome using SP1 transcrition factor binding site from Postion Weight Matrix

I have a list binding site motif of SP1 transcription factor which collects from PWMScan tools. Actually this tool scan whole human genome and give the entire binding motif list. From that list of ...
1
vote
0answers
133 views

Can Mauve export indels or is there an whole-genome aligner that can export indels?

I have aligned two whole genomes of the same species in Mauve using progressiveMauve. One of the genomes is 2 megabases longer than the other so I know it must contain some insertions. Looking at the ...
0
votes
0answers
8 views

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 ...
0
votes
0answers
27 views

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 ...
0
votes
1answer
111 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? ...
0
votes
0answers
22 views

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, ...
0
votes
0answers
101 views

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 ...
0
votes
0answers
9 views

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 ...
0
votes
0answers
18 views

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 ...
0
votes
0answers
51 views

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 ...
0
votes
1answer
258 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?
0
votes
0answers
200 views

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. ...
0
votes
0answers
66 views

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 ...
0
votes
0answers
37 views

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 ...