Questions tagged [sequence-annotation]
The process of attaching contextual information to a biomolecular (DNA, RNA, or protein) sequence, such as the location of genes, promoters, or repeats in genomic DNA, or the function of a protein.
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How Can You Reformat an OTU Table from qiime2 pathway to Include Sequence IDs?
I am trying to run Tax4Fun in MicrobiomeAnalyst, but am running into trouble with my table formatting. From the qiime2 pathway, I have an OTU, metadata and taxonomic table formatted like so:
In ...
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PROKKA setupdb / cmpress error
I am trying to run --setupdb in Prokka, but I'm getting this error that I can't seem to find the answer for.
When I run
prokka --setupdb
I get
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What tool(s) can I use to use a .faa file to feed into JSMol?
JSMol, the molecular modelling software, requires PDB file format to work and render the graphics. Currently, I am writing an annotation software - backend in Perl - that takes in a .faa file (fasta ...
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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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Barrnap Bacterial rRNA Predictor script permission denied error when running Prokka
I am trying to run the Prokka annotation tool on my linux machine and have installed Barrnap and added it to $PATH and given the folder chmod 777 permission. However, when running Prokka, it gives the ...
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Sanger sequencing annotation error
I am a student in a Cancer lab. Working with sanger is new to me. While analyzing a report we found an insertion that has not been reported in any databases so far, we were working on checking if the ...
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I have a partially described gene from a plant, which tool may I use for predicting regolatory and UTRs sequences from a single DNA fragment?
I have a partially described gene from a plant with CDS and 3'UTR described but no 5'UTR; if I know the locus and upstream and downstream regions, is there a tool I can use for predicting regulatory ...
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In VEP annotation, how is the codon field interpreted?
After annotating with VEP a VCF file, we obtain different fields. One of them is called Codons which represents the affected codon in the transcript of the gene. ...
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Why do Illumina 850k/EPIC arrays ignore CpGs which are "GC" in the forward strand?
CpGs are symmetrical, in that a CG sequence on the forward strand is hybridized to a GC --- and both dinucleotides on each opposing strand are CpGs dinucleotides which can be methylated. Conversely, ...
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conversion of a gbff file to a gff file
I want to get the annotations in gff format for a assembled genome. But for some species there is no available annotation in gff format in NCBI but only in gbff format. And I don’t know how to convert ...
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What does it mean when a gene and its transcript have opposite orientations in a GFF3 file?
I was working with a given GFF3 file, and I observed that some transcripts have orientation opposite to their transcripts. Here is a snippet:
...
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Get genome coordinates from UniProt entry?
I'm trying to get genome coordinate information programmatically for multiple genes.
As an example, I'd like to get the annotation (list of exons and their chromosomes, starts, and ends) for this ...
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How can I assemble my genome from raw files?
I've had my whole genome sequenced (at 30x average coverage) by a lab, and they have provided the raw files to me (BAM, FASTQ, and VCF).
How can I assemble it?
And does assembly provide any further ...
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Gencode PolyA feature annotation GTF gene_id not the same as Comprehensive gene annotation GTF
I have downloaded the Gencode PolyA feature annotation GTF here. The first 10 lines are like this:
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Find a genomic coordinates for a protein aminoacid position
Is there a function that can map genomic position (hg19) back from a protein position? I can have name of a particular transcript, and exon number.
For example, I have KRAS gene for which I would like ...
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snpEff annotation and variant in a gene
I'm using snpEff to annotate genetic variants. However, the annotation often returns more than one annotation (see below for an example):
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Different line length in fasta file
I am currently using VEP for variant annotation.
I am facing an error as below:
[E::fai_build_core] Different line length in sequence 'Pn9'
I understand there is ...
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How to remove redundancy from a gtf file?
I have an annotation file. I would like to remove redundancy, as shown in the example (in the real file, I have a lot of these redundant cases).
I would like to consider only one of the following ...
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How can I get latest .vcf files with annotation data?
I'd like to perform the annotation (1000genomes, COSMIC etc.) of my variants using SnpSift and SnpEff, however so far all I get are vcf files for separate chromosomes:
http://ftp.1000genomes.ebi.ac.uk/...
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On the same strand, for the same gene, can exons be overlapping?
I want to get a set of exon regions for each protein coding gene.
I extracted a set of relevant information (chromosome, start, end, gene ID, gene name, gene type, exon number and exon ID) from a GTF ...
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BPGA error: there was no protein data in file
I'm trying to do pan-genome analysis using BPGA and I face this error:
This error didn't show up in the other data set where all the .gbk is downloaded from NCBI. This .gbk file is our own data and ...
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Why does gene count increase drastically after scaffolding with Hi-C data?
I have a conceptual question.
I have a diploid, outcrossing plant genome assembly of ~1.1 Gb size. The original assembly is generated from PacBio reads. After genome annotation with the ...
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Find the genomic locations of exons of certain human gene
So I know Consensus CDS has the genomic locations of exons, however, only of the exons in the CDS. Everything before or after is not included.
NIH variation viewer has those (kinda-) radio buttons ...
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How to get a list of all human morphogens?
Gene Ontology provides many genes annotated as taking part in various morphogenesis processes but I want to get a list of all morphogen coding genes specifically. Uniprot does not have "...
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An error with annovar
I want to install annovar but in one particular part I always get this error
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Correspondence of SARS-CoV-2 annotations (Nextstrain clades - Pango lineages)
Is there any annotation file providing correspondence between Nextclade and Pangolin variant nomenclature/annotations, to annotate some SARS-CoV-2 genomes from Gisaid with both these?
For the moment I ...
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replacing periods with hyphen
I am a software engineer and not a bioinformatician. I am looking at some code where they are looking at aligned proteins that are in the A2M alignment format (https://compbio.soe.ucsc.edu/a2m-desc....
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What does 'Human Alternative sequence Gene' mean in Ensembl?
I have downloaded a dataset containing RNA-Seq RPKM (reads per kilobase per million) values for 52376 genes (in humans). To find RPKM values for the gene KIR2DL2 in the dataset, I have to search for ...
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Does anyone know what tools are used to construct this beautiful genome map?
Does anyone know what tools are used to construct this beautiful genome map?
The research paper didn't mention how to construct this map.
Link to paper: https://www.sciencedirect.com/science/article/...
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Ensembl Variant Effect Predictor (VEP) issue during execution
I got this error during execution, pls guide me.
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How to train annotations tools
I would like to train Augustus, SNAP and GlimmerHMM. I found protein sequences in GenBank and orthodb.org. Furthermore, I found HMM files on busco-data.ezlab.org.
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Demovir produces an empty output
I am new to bioinformatics and am working on viral metagenomic (virome) datasets and so would like to use Demovir* for doing taxonomic annotations on my viral contigs.
First, I installed all ...
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Transfer annotations from one genome assembly to another
I've got an annotated draft genome assembly made using short and long read strategies. I've also done optical mapping to stitch some of the contigs together, with the goal being chromsome-length ...
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Problem with Seurat reference mapping
I have 10X scRNA-seq multiome's 3' poly-A capture (scRNA-seq+ATAC-seq) from PBMC
Using Seuratreference mapping, I mapped my scRNA-seq part on reference PBMC (for ...
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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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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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Genome annotation
I have helped a lab sequence a mitochondrial genome. I used then MITOS to annotate the genome (warning them that I did it just for curiosity as I am not experienced). They submitted the sequence and ...
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Hg38 annotation tracks retrieval
I want to retrieve an annotation object (as GRanges) containing different UCSC annotation tracks such as CpG Islands, TSS, TFBS and promoters for hg38 Human reference genome. But "UCSC Genes"...
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Annotating a .vcf with centimorgan information
Some programs (e.g. shapeit4) automatically annotate an INFO tag into a .vcf file which gives the cumulative genetic distance in cM between each SNP:
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SnpEff not correctly annotating multiple-nucleotide polymorphisms
I have some SARS-CoV-2 sequencing data that I'm trying to annotate with SnpEff, however SnpEff doesn't appear to be recognizing multiple adjacent SNPs within the same codon and correctly calling them ...
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Annotating gene names or gene IDs to a dataframe containing SNPs?
I have a large data-frame (excel file) of SNPs with genotyping data. I need to filter the data to get SNP information of a specific gene alone. The list is too long to do it manually. I was wondering ...
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Finding annotated counterpart after BLASTn with efetch (Biopython)
I am creating a pipeline for the identification of unknown transcripts. After a local BLASTn search of the transcripts, I have a large list of the respective hits with different genomes. I have the ...
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How to identify genes from a genome assembly of C. Elegans?
I have two full genome assemblies for C. Elegans samples collected from two different geographical areas that I found on WormBase. These are in fasta format. I want to go gene-by-gene and compare the ...
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Do RepeatModeler results contain functional domains?
The repeat families predicted by RepeatModeler contain known transposable elements (TEs) and unknown ones.
How do we know whether some of these may actually:
within a functional domain of a gene or
...
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How to programmatically classify a protein according to its genbank feature
Say I found an interesting protein in a genbank file, e.g.:
...
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How to annotate optimally a fungal genome without RNA-seq evidence?
Genome information：
~50M nt
2300+ contigs
No pre-trained parameters in Augustus
There are several well annotated RefSeq genomes of this genus.
There are several RNA-seq data of this genus, but not in ...
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Prokka error message
I am trying to run Prokka but the following error message appears:
Could not run command: makeblastdb -hash_index -dbtype prot -in /cluster/software/prokka/1.13.7-gompi-2019a/db/kingdom/Archaea/sprot ...
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annotation using ChIPseeker package error
I have differential binding sites object obtain from diffBind (dba.report). I am using the ChIP Seeker package to annotate the peaks but keep getting the following error: Error in (function (classes, ...
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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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UTR features in gbk files
I have a gbk files for a viral genome that I have used biopython to add features of the 3' and 5' ...
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