9 votes
Accepted

Converting gene names from one public database format to another

I tend to use Ensembl Biomart for such queries since there are APIs for various programming languages, e.g. biomaRt, and, maybe more interestingly, via a REST API (although it’s a pretty terrible one)....
8 votes

Converting gene names from one public database format to another

If you're comfortable doing a little programming, check out mygene.info (web services for gene annotations of all sorts). ID translation is specifically one of the use cases addressed in the ...
  • 81
7 votes

Converting Ensembl Gene IDs to Entrez Gene IDs through biomart

Conversion using R: ...
  • 2,584
7 votes
Accepted

Missing data mappings in mygene.info while trying to convert Genes Ensembl Ids to Entrez Ids

As others have mentioned in their answer, bioMart is usually the best place to go for this infomation because it draws its data directly from the Ensembl database. However, you will find you do not ...
  • 3,221
6 votes
Accepted

Convert Reactome Protein IDs to Pathway IDs?

If you don't mind hitting it 50k times and are OK with python3... ...
  • 19.3k
6 votes
Accepted

Converting Ensembl Gene IDs to Entrez Gene IDs through biomart

The ID you need is the NCBI gene ID, which is the same as the EntrezGene ID.
  • 3,221
4 votes

Converting gene names from one public database format to another

You can do the same using AnnotationDbi Package from Bioconductor. Download the organism specific annotation file like org.Mm.eg.db for mouse and map current gene ids to the gene names/gene symbols.
  • 584
3 votes

How to convert data in gmt format to dataframe?

Ok. Answering my own question. I did this way. And I got the output I want. ...
  • 621
3 votes

How to convert amino acid sequence to SMILES format

SMILES are meant for machines, but reading up on the format is very handy and one totally can read and write them —I do it often and could not recommend it enough. You can have SMILES written ...
  • 3,854
3 votes

Converting gene names from one public database format to another

I'm not a huge fan of the Ensembl BioMart system because I find it difficult to use. The Synergizer has a very straightforward interface and works pretty well for most lists. Note: it hasn't been ...
3 votes

Converting gene names from one public database format to another

My favourite gene database conversion site is db2db. You provide a list of IDs in one of a large number of different public formats, and can select one or more IDs as translation targets. It will then ...
  • 12k
3 votes

Convert Reactome Protein IDs to Pathway IDs?

On Reactome website they have at the download page mapping files (uniprot, ensembl, etc.), but unfortunately not for the protein IDs you are using (stable identifiers). I had contact with their ...
  • 3,551
2 votes

Entrez or Ensembl gene IDs?

I think there is no general answer to your question. Which type of ID you will use depends on how practical it will be for your downstream processing. This depends on what other source of information ...
  • 3,030
2 votes

Converting gene names from one public database format to another

By far my preferred option for doing this manually is PICR: http://www.ebi.ac.uk/Tools/picr/ BTW it is not "ridiculous" to get different numbers of genes reported for a given set of proteins. For ...
  • 356
2 votes

need bam file for pilon

Run a short-read mapper. For example: bwa index assembled.fasta bwa mem -pt16 assembled.fasta read1.fq.gz read2.fq.gz \ | samtools sort -m4G -@4 -o align.bam -
  • 6,023
1 vote
Accepted

convert GT:PL format to GT:GP format

Currently you have phred-scaled genotype likelihoods or PL values. Genotype likelihoods give the likelihood of observing the read data (i.e. the number of reads which map to either the ref or alt ...
  • 1,290
1 vote
Accepted

converting mouse genes to human genes

Mice genes are usually the same as the human ones, but lower case with only the first character as upper (Sox17 -> SOX17). <...
  • 507
1 vote

What is the best way to programmatically convert Ensembl ids from one release to other? e.g. transcript ids from release 75 to 100

The ID history converter is available as a Perl script. This script accesses these MySQL tables, so you could query these tables directly. Note that the mapping session is only one release at a time, ...
1 vote

How to convert data in gmt format to dataframe?

You can use GSA.read.gmt function from GSA package. The following code can be used to convert the file to a dataframe. Just ignore the warnings. Original_response ...
1 vote

How to convert data in gmt format to dataframe?

You can import the csv file as a table. This does not require further libraries: ...
  • 320

Only top scored, non community-wiki answers of a minimum length are eligible