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.

Filter by
Sorted by
Tagged with
2 votes
1 answer
58 views

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 ...
0 votes
1 answer
23 views

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 ...
2 votes
0 answers
25 views

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. ...
  • 1,035
1 vote
1 answer
32 views

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, ...
  • 131
1 vote
0 answers
19 views

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 ...
3 votes
1 answer
27 views

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: ...
2 votes
2 answers
71 views

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 ...
1 vote
3 answers
67 views

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 ...
1 vote
1 answer
63 views

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: ...
3 votes
1 answer
67 views

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 ...
  • 203
1 vote
0 answers
77 views

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): ...
  • 153
1 vote
1 answer
121 views

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 ...
3 votes
0 answers
103 views

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 ...
  • 141
1 vote
2 answers
83 views

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/...
  • 206
4 votes
1 answer
98 views

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 ...
  • 1,773
1 vote
1 answer
73 views

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 ...
  • 121
1 vote
0 answers
20 views

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 ...
2 votes
2 answers
54 views

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 ...
1 vote
0 answers
17 views

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 "...
0 votes
0 answers
38 views

An error with annovar

I want to install annovar but in one particular part I always get this error ...
  • 1,743
3 votes
2 answers
136 views

Correspondance of SARS-CoV-2 annotations (Nextclade - Pangolin)

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 ...
  • 2,656
1 vote
1 answer
39 views

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....
  • 113
0 votes
1 answer
203 views

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 ...
  • 159
3 votes
3 answers
153 views

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/...
  • 121
1 vote
1 answer
168 views

Ensembl Variant Effect Predictor (VEP) issue during execution

I got this error during execution, pls guide me. ...
  • 11
1 vote
0 answers
27 views

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. ...
2 votes
1 answer
48 views

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 ...
1 vote
1 answer
100 views

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 ...
  • 11
0 votes
1 answer
73 views

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 ...
  • 1,743
2 votes
1 answer
66 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 ...
0 votes
0 answers
28 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, ...
  • 43
0 votes
2 answers
92 views

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 ...
2 votes
1 answer
47 views

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"...
  • 21
4 votes
1 answer
153 views

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: ...
  • 1,390
1 vote
0 answers
78 views

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 ...
  • 249
0 votes
1 answer
121 views

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 ...
1 vote
0 answers
29 views

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 ...
  • 26
1 vote
1 answer
79 views

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 ...
  • 113
4 votes
0 answers
30 views

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 ...
2 votes
1 answer
66 views

How to programmatically classify a protein according to its genbank feature

Say I found an interesting protein in a genbank file, e.g.: ...
1 vote
1 answer
76 views

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 ...
  • 81
1 vote
0 answers
370 views

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 ...
1 vote
1 answer
352 views

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, ...
  • 95
1 vote
1 answer
541 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. ...
1 vote
0 answers
81 views

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' ...
  • 143
1 vote
0 answers
17 views

Finding the relevant annotations for biomarkers

I am looking to find a way to map a list of biomarkers of interest, say genes or bacterial functions, to existing annotation databases. Usually this is done in reverse, as such that based on ...
2 votes
0 answers
24 views

Finding original papers for gene annotations

I am wondering if there's a database to look up the annotation history of an arbitrary gene/ORF, with links to the primary literature for each step of the annotation. I have found that neither NCBI ...
  • 131
0 votes
1 answer
40 views

Inheritance annotation for nsSNPs

I am relatively new to SNP analysis. Is there a database to find annotation about the Mendelian inheritance of SNPs? I have a small list of nsSNPs (non-synonymous SNPs) and I need to find how they are ...
1 vote
0 answers
36 views

BAM file filteing to remain best isoform

I ran HiSat2, MarkDuplicate, removed reads with the lower quality score than 40 and finally only kept properly paired reads. After the BAM filtering steps, I used the Scallop results with TransDecoder....
2 votes
1 answer
10k views

Changing active.ident in Seurat

Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was working but the new one isn'...