24 votes
Accepted

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

To add to rightskewed answer: While it is true that: Gencode is an additive set of annotation (the manual one done by Havana and an automated one done by Ensembl), the annotation (GTF) files are quite ...
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  • 504
14 votes

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

Dfam has recently launched a sister resource, Dfam_consensus, whose stated aim is to replace RepBase. From the annoucement: Dfam_consensus provides an open framework for the community to store both ...
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12 votes

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

Ensembl vs Gencode https://www.gencodegenes.org/faq.html The GENCODE annotation is made by merging the Havana manual gene annotation and the Ensembl automated gene annotation. [...] In practical ...
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9 votes

Tools to create annotated table of variants from VCF

Hail might be an option for you. It is actively developed by a growing team at the Broad. It is rigorously tested (continuous integration, continuous deployment, bug reports get regression tests, ...
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9 votes
Accepted

5'UTR and 3'UTR annotation in yeast

I am unaware of any "official" or gold-standard UTR annotations in S. cerevisiae. One option is to use the annotations from the TIF-Seq publication (Pelechano et al. 2013). The ...
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  • 1,498
8 votes
Accepted

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

Here's a Perl script that can do this: ...
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  • 8,111
8 votes

Same transcript coordinates in gtf file, different transcript ID

As Ian explained, these are different transcripts which happen to have the same start and end positions. You have no information on their exonic structure in that file. However, if you look them up at ...
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  • 8,111
8 votes

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

You may try to set the correct path through the infernal_dir variable in tRNAscan-SE.conf.src. You might need to do this before ...
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  • 2,960
7 votes

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

For pre-existing reliabe TE libraries it is a bit of a mess, because not everybody deposits the species-specific TE libraries to a database like RepBase. And as far as I know DFAM contains only human ...
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7 votes

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

N.B., I'm avoiding discussion of "best", since that's more or less impossible to answer. Your question can actually be divided into two: What's a good tool for pathways analysis (ideally in R)? What ...
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  • 19.2k
7 votes
Accepted

Same transcript coordinates in gtf file, different transcript ID

transcript objects cover the co-ordinates from the start of the first exon to the end of the last exon of a transcript (i.e. an isoform). If two different isoforms ...
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  • 3,211
7 votes
Accepted

Retrieve detailed gene descriptions

MyGene.info Using the R package for the MyGene.info database: ...
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  • 2,574
7 votes

Retrieve detailed gene descriptions

Description of how to use biomaRt here. Filter by your list of gene IDs. Get the descriptions etc as attributes. Eg: ...
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7 votes

5'UTR and 3'UTR annotation in yeast

I found the following two files in https://downloads.yeastgenome.org/sequence/S288C_reference/: SGD_all_ORFs_3prime_UTRs.fsa SGD_all_ORFs_5prime_UTRs.fsa According to the README files in the same ...
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  • 8,111
6 votes

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

With a k-mer size of 28 it shouldn't be finding that many matches. And the prokka results are suspicious as well. Maybe you have multiple contigs (none larger than 100kb) in that file? What is the ...
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6 votes

Basic questions about GSEA

Use the following R package for Gene Set Enrichment analysis of RNA-seq data: seqGSEA There is another R package (fgsea) recently published called "Fast Gene Set Enrichment Analysis" by Alexey ...
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  • 584
6 votes

Basic questions about GSEA

You seem to refer to the GSEA provided by the Broad institute, (there are other GSEA algorithms). 1) You can provide whatever you wish, but if you want to know if those gene sets in which side of ...
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  • 4,602
6 votes
Accepted

How to calculate overlapping genes between two genome annotation versions

Short Answer: In my opinion, my approach would be to pull out the CDS exons and run bedtools on those. A Few More Details: When you pull out the exons, make sure that you assign them all IDs if the ...
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  • 346
6 votes

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

If you are still interested, last year miRBase generated new updates. Currently, according to ftp site the last release is 22.1. So, it is not a dead project and for more specific information you ...
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6 votes

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

To add practical advice to what others have said: In a practical sense, I think the biggest difference between RefSeq and Ensembl/GENCODE is in the sensitivity/specificity trade off. Ensembl aims ...
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  • 3,211
6 votes

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

You don't really need to get around anything, your example can be loaded correctly with read.delim(). The rows with missing values are filled in with blanks. You ...
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  • 19.2k
5 votes

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

While your question is specific to cancerous germline mutations, I'd suggest you look at the COSMIC database of somatic mutations to include in your analysis. There are other factors to include in ...
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5 votes

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

You could use RepeatScout, which has defined repeat libraries for a limited number of species (including human, mouse, and rat). If your taxon is not represented, you can also do de novo repeat ...
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  • 3,462
5 votes

How to transfer gff annotations in genome with extensive duplications?

There is one very simplistic way I use which might work for what you are doing, it is similar to what terdon proposed. Take a de-novo microbial genome annotation tool (I have my own, but you could ...
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  • 744
5 votes
Accepted

Tools to create annotated table of variants from VCF

I have used FEATnotator and I think it can provide all of the columns you would like to see. There are many output files generated, but the consolidated output has the following columns: Chromosome ...
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  • 128
5 votes

Tools to create annotated table of variants from VCF

snpEff is a great tool for annotating VCF files and you can add custom reference sequences. http://snpeff.sourceforge.net/ Guide to add custom annotation files in snpEff https://gatkforums....
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  • 584
5 votes
Accepted

hg38 GTF file with RefSeq annotations

You will probably be interested in the following UCSC wiki page, which explains how to go from most of the UCSC tables to GTF/GFF: http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format The ...
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5 votes
Accepted

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

Author here - this was a bug which was fixed in August: See the issue in Github. You will need to use the latest Github HEAD version until the next release.
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  • 66
5 votes
Accepted

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

The GFF3 file format specification doesn't care where annotations are described in the file, although it can make some things easier if the annotations are ordered by the start position: ...
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  • 11.7k
4 votes

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

You requested a tool similar to PANTHER but in R. First, the PANTHER (Protein ANalysis THrough Evolutionary Relationships) tool does a classification based on evolutionarily related proteins, gene ...
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  • 4,602

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