Questions tagged [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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40
votes
5answers
8k views

Feature annotation: RefSeq vs Ensembl vs Gencode, what's the difference?

What are the actual differences between different annotation databases? My lab, for reasons still unknown to me, prefers Ensembl annotations (we're working with transcript/exon expression estimation)...
17
votes
6answers
2k views

Are there any RepBase alternatives for genome-wide repeat element annotations?

I’m using the RepBase libraries in conjunction with RepeatMasker to get genome-wide repeat element annotations, in particular for transposable elements. This works well enough, and seems to be the de ...
12
votes
1answer
251 views

How to calculate overlapping genes between two genome annotation versions

I have two annotations of the same genome generated with different annotation pipelines. I want to identify overlapping gene models. An important feature of this genome is that there are many 'genes ...
9
votes
3answers
948 views

Tools to create annotated table of variants from VCF

The problem: I have a VCF file, a reference genome, and a bunch of annotations for the reference (genes, repeat regions, etc.) as GFF or BED files. What I would like is a tool that takes all of this ...
9
votes
2answers
292 views

How to transfer gff annotations in genome with extensive duplications?

Microbial genomes can contain extensive duplications. Often we'd like to transfer annotations from an annotated species to one that is newly sequenced. Existing tools (e.g. RATT, LiftOver, Kraken) ...
8
votes
2answers
1k views

5'UTR and 3'UTR annotation in yeast

I am working on a project in which I need to compute several parameters (such GC content and length) of 5'UTR and 3'UTR sequences of Saccharomyces cerevisiae yeast genes. The problem is finding a ...
8
votes
2answers
278 views

Comparing two genome annotations

I have one-dimentional array (human genome). Also I have two annotations for it, we can think about them as different peaks (it's nucleosome and secondary structures). How can we find correlation and/...
7
votes
3answers
2k views

How to perform functional analysis on a gene list in R?

From an RNA-seq experiment I have about 17000 gene ids for 2 sample conditions arranged according to their log2 fold changes when compared to a control. I need to annotate these, but I've never done ...
7
votes
1answer
676 views

How can I create my own GO association file (gaf)?

This question is based on a question on BioStars posted >2 years ago by user jack. It describes a very frequent problem of generating GO annotations for non-model organisms. While it is based on ...
7
votes
1answer
812 views

Where to download JASPAR TFBS motif bed file?

I am interested in determining if any transcription factor binding site motifs are enriched in some BED files from a DNA methylation experiment. I am looking for a database that has BED Files ...
6
votes
2answers
407 views

Same transcript coordinates in gtf file, different transcript ID

I have a gtf file from Ensembl, and I noticed that several "transcript" annotations have the exact same coordinates. See for instance the third and fourth transcripts ("Y74C9A.2b.1" and "Y74C9A.2b.4") ...
6
votes
4answers
436 views

Identify non-coding regions from a genome annotation

I have this GTF file and I use the command below on a Linux machine to extract the coding regions of the genome: ...
6
votes
1answer
98 views

Bacterial genome annotation of a clinical isolate strain?

So I'm basically so new to this that I'm just trying to find out what tools, methods, and keywords I should go look up by myself. I have a unique strain of a bacteria. I was given RNAseq data for ...
6
votes
2answers
455 views

Transcript Coordinate Ranges to Genomic Coordinates

I have 2 GFF3 files: Features using transcript IDs as the landmarks. i.e. "CDS" feature types using coordinates from transcript space. Features using chromosome IDs as the landmarks. i.e. "exon" ...
5
votes
4answers
1k views

tRNAscan-SE error: FATAL: Unable to find /usr/local/bin/cmsearch executable

I have downloaded tRNAscan-SE from here. After decompressing and untaring the file, I installed it using: ./configure make make install When I type ...
5
votes
5answers
161 views

Where is an up to date miRNA database and what happened to miRBase?

miRBase 21 was published June 26, 2014 and was still in its growth phase. Why is it not being updated anymore or the project declared officially dead? ENSEMBL also uses miRBase as a starting point (...
5
votes
3answers
3k views

Retrieve detailed gene descriptions

Given a list of gene IDs, how do you retrieve the gene description, summary and other detailed information in R?
5
votes
2answers
657 views

Difference between de novo transcriptome assembly methods

I have been looking around (including read the original papers) to understand what is essentially the difference between StringTie in non-reference based mode (de novo) and Trinity de novo assembly. I ...
5
votes
1answer
2k views

hg38 GTF file with RefSeq annotations

I'm not sure what I'm missing, but I'm struggling to find an official hg38 GTF file with RefSeq annotations. I'd like to provide ...
5
votes
1answer
377 views

Derive a GTF containing protein coding genes from a GTF file with Exons and CDS

Why I need a compatible file I’m trying to run velocyto with the R package to analyse RNA velocity (cell trajectories) with single cell RNASeq data. I have performed single cell analysis from 10x ...
4
votes
4answers
93 views

In GFF3, annotating more than one protein-coding gene (i.e. polycistronic) contained in a eukaryotic mRNA

Below is an example of a simple GFF3 file: ...
4
votes
2answers
107 views

How can I use annotations to remove variants not relevant to cancer risk?

I currently have ~180 whole germlines and around 10M SNPs/indels. I would like to build a predictive model using Machine Learning (ML) techniques to predict cancer risk according to these germline ...
4
votes
1answer
238 views

Keep Format and Individual fields when annotating VCF with VEP

I'm currently updating my Variant Calling Pipeline by switching the VCF annotating software from Annovar to VEP for a variety of regions, not least how easy it is to annotate with HGVS notation and ...
4
votes
2answers
116 views

How to predict stop codons in Illumina reads?

I have Illumina MiSeq paired-end reads from 150bp amplicons mapped to my reference genome (> 1000X coverage). These reads have indels that may or may not induce frameshifts. If the indel induces a ...
4
votes
1answer
608 views

get gene lines from gtf file

I would like to retrieve gene lines from a GTF file for which I only have exons & transcripts lines (output from Cufflinks) and alternative splicing possible. I need gene lines for compatibility ...
3
votes
5answers
184 views

Import a tab-separated file with differing numbers of elements in each row; prokka output

I am using prokka to annotate a bacterial genome: prokka ecoli.fa Prokka is outputting a tab-separated file (called PROKKA_12142017.tsv) with differing numbers of ...
3
votes
4answers
433 views

Basic questions about GSEA

I'm currently learning about Gene Set Enrichment Analysis (GSEA) in the hopes of using it in my analysis of differentially expressed genes, and I just had a few questions about the program, ...
3
votes
4answers
173 views

Purpose of ### (3 consecutive pound signs / hashtags / octothorps) in GFF3

I downloaded the annotation of the C. elegans genome in GFF3 format from Ensembl. I typed the following command, hoping to get the header of the file (lines starting with ...
3
votes
1answer
141 views

Why do BLASTn and prokka not seem to be searching the whole fasta file?

When I use blastn and prokka (I will detail exactly how I did so below) on a 2.8 million bp fasta file I get output start/end numbers that do not seem to cover the entire genome. Starting with a ....
3
votes
1answer
188 views

What does the number mean in an HGVSp annotation?

Let's take the example p.Arg452Pro that I got from an annotated VCF file that contains an HGVSp column. What does ...
3
votes
1answer
58 views

TRAL does not find “Phobos result file”

I want to use TRAL to annotate tandem repeats in the reference genome of Caenorhabditis elegans. For this, I need to install some external software, such as Phobos. I've downloaded Phobos and I am ...
3
votes
2answers
377 views

How can I find the chromosomal location of a list of genes?

I have a list of genes nearly 20000: gene name (column1) and coordinates (columns 2 and 3) ...
3
votes
2answers
140 views

Generate SNP/indel annotation in Arabidopsis

I have a genome-wide list of germline SNPs and short indels for Arabidopsis thaliana, which I generated with Varscan. Regardless of the tool used to generate them, I would like to annotate them, i.e. ...
3
votes
1answer
313 views

Annovar index out of date

I'm trying to use Annovar to annotate some variants with their CADD and FATHMM scores. I've downloaded the latest versions of the software and the databases but when I run it I get an error saying the ...
3
votes
1answer
29 views

Batch detection of CRISP proteins in fasta file

Probably a naive question. I am inexperienced. I am interested in identifying potential CRISP (Cysteine-rich secretory proteins) in a certain tissue transcriptome (ca. 20k sequences in fasta). I ...
3
votes
1answer
47 views

Syntenic gene browser

I found that there is a Syntenic gene browser at GEvo. Do anyone know where could I find a similar browser for a local installation?
3
votes
0answers
40 views

Why does repeatmasker annotate transposons of length 1?

I am working on Mac OSX. I have downloaded RepeatMasker from www.repeatmasker.org. I have downloaded RepBase from www.girinst.org. I have download the WS266 version of the C. elegans genome from ...
3
votes
0answers
156 views

Get genomic coordinates using GenomicFeatures by HGNC gene names

I want to get coordinates of human genes from my list (consisting of hgnc genes id) using GenomicFeatures and TxDb.Hsapiens.UCSC.hg19.knownGene R packages from Bioconductor. ...
2
votes
2answers
248 views

seqret error when trying to transform GFF3 and FASTA files into EMBL format

I am using the tool seqret from emboss to transform an annotation file in GFF3 format and a FASTA file into an EMBL file because Wormbase does not supply an EMBL file with annotation and sequence ...
2
votes
3answers
222 views

Modifing a GFF3 file and writting to a new file

I modified the GFF3 file with the below code: ...
2
votes
4answers
119 views

Merging two .txt files

I have two .txt files and let's call it 'File A' and 'File B.Here are examples of what file A and file B looks like: FILE A ...
2
votes
1answer
68 views

Obtain CD (cluster of differentiation) marker expression information

There are 394 CD marker genes. Various resources (BD handbook, Abcam guide) contain information about which cell types express which CD markers. What is the best way to obtain or download this data so ...
2
votes
2answers
129 views

RepeatMasker annotation

I collected my own denovo library using many different tools Pipeline (structure-based ) and I updated all the headers corresponding to RepeatMasker format, to obtain Repeat coverage in the genome and ...
2
votes
1answer
81 views

scRNASeq expression matrix with decimal values

I am trying to replicate some results of a scRNASeq experiment and, when I looked at the data provided by the author, I noticed that some of the counts in the expression matrix are represented as ...
2
votes
1answer
78 views

Problem installing RATT

I have followed the steps here to install RATT, i.e.: svn co "https://svn.code.sf.net/p/ratt/code/" ratt-code However, when I check my installation by running '$...
2
votes
1answer
55 views

where to find pathogenicity metadata for E.coli genomes

I have a list of about 900 E.coli genome ids (Genbank plus NCTC ids), e.g.: ...
2
votes
1answer
54 views

Adding an attribute to GFF3 file

I failed to add Note=Gene description to mRNA attribute with the below code: ...
2
votes
1answer
24 views

In SBOL, when should I annotate a DNA sequence vs. making sub-components?

When representing a DNA sequence in SBOL as a ComponentDefinition, you can mark things like promoters and coding sequences in two different ways: either as a ...
2
votes
1answer
47 views

No refseq transcripts in 2nd half of Y chromosome for HG38

Obviously there is a gap in my understanding of how sex chromosomes are annotated. I've been working on some CNV calls and noticed that most of the 2nd half of ChrY is missing annotations and no reads ...
2
votes
3answers
960 views

Annotation with Prokka or RAST.

I was experimenting Prokka and RAST annotation tools. So, I took a well-annotated swinepox virus genome from genebank (NCBI Reference Sequence: NC_003389.1). I ran those sequences on Prokka and RAST ...