We're currently using a variety of different versions of a variety of different organism reference genomes and are often running into the need to convert between chromosome coordinate naming systems (e.g., when someone wants data aligned against the hg19 reference from ensembl and for a gencode GTF file to be used). This is often as simple as a quick add/remove of "chr", but not always (e.g., who would know that JH806595.1 in gencode is HG1441_PATCH in ensembl?). So, does anyone know of a nice resource somewhere that provides the mappings?
At the end of the day, I just need a tab separated file with the name mappings. I've already written a little python script to perform all of the conversion (a trivial task), but making the mapping files is proving to be a PITA and I assume someone else has already done this.
Edit: BTW, if I have to make the mapping files myself I'll put them on github. It's absurd for that to ever need to be repeated by anyone.
Edit: For what it's worth, at least some of the hg19 gencode<->ensembl mappings are here.
•
written
by
Devon Ryan
3 answers
Should someone ever need this sort of thing in the future, I've started a github repository with a few conversions here. Everyone is encouraged to add additional conversions or fix any errors they see in those already there. Just submit a pull request.
I'll likely add more of these over time as we actually need them (I still need to add some for the fruit fly genome).
The original information comes from the genome assemblies deposited in NCBI. There are multiple names for each contig therein. The trick is simply to figure out who uses which column (sometimes they like to modify them further).
That's unfortunately not the case.
•
written
by
Devon Ryan
True, unfortunately some users complain if things aren't processed exactly as requested, even if just using Ensembl (my preferred solution!) produces the same results.
Hi Emily, I understand that but why there is a difference in gene counts between Gencode and Ensembl, can you please have a look at this question I recently posted.
•
written
by
Veerendra Gadekar •
Hi,
I went to your github repository to access these conversion tables, thank you this is very useful.
I am very new at bioinformatics and I am currently trying to convert the ENSEMBL chromosomes names of an annotation gtf file to UCSC chromosomes names, in order to index them with STAR (the STAR manual specify that the chromosome names of the fasta file and the gtf file should be the same)
But then, the only thing I have to do is to replace the names in the gtf annotation file, by their UCSC equivalent, and then I can run my indexing?
It's a trivial question but I am really new to all of this, Thank you very much,
Camille
Download the fasta file from Ensembl instead and save yourself the hassle. You can get the whole bundle from iGenomes, but that'll be a larger download.
Log in to answer this question.
-
Request to validate my RNAseq workflow
written by umn_bist •
-
Using ensembl genomes and gtf conversion
written by as9309 •
-
Filter blastn results by kingdom
written by user230613
-
Can someone give insight into the difference between current gene-function databases?
written by VermillionAzure •
-
Getting all Ensembl protein lengths
written by Natasha Latysheva •
-
BRIG finding errors with genbank file for annotation/ do I need to edit genbank file?
written by fernan23 •
-
Missing BLAST hits - max_hsps and max_target_seqs?
written by glenn •
-
Get Fasta File With Protein Sequences Given Entrez Gene Ids
written by Stephen
-
Converting Ensembl Gene Ids To Hgnc Gene Name / Coordinates
written by Ryan D
-
Comprehensive Gene Sets
written by Sequencegeek •
I wrote a tool using to compare chromosomes using MD5: http://plindenbaum.blogspot.fr/2013/07/g1kv37-vs-hg19.html could that help ? mappings: https://github.com/lindenb/jvarkit/tree/master/src/main/resources/chromnames
It wouldn't be so useful in this case, since I need this for GTF/BED/etc. files. Though it's good to know about that tool!