NGSDImportEnsembl: fix SNORD118 transcripts on several chromosomes

[alex-seitz]

Hi, we realized an error on the parsing of the Ensembl into the NGSD database. There are several genes in the gff-file named U8.1 up to U8.22. These are different genes on different chromosomes. Apparently the gene SNORD118 has an alias of U8 and somehow all of these transcripts are matched with the SNORD118. Additionally, the gene U8 apperears more than once in ENSEMBL, e.g. under the following IDS: ENSG00000199713 ENSG00000239148

Is there any way to remedy this?

Best, Alex

[marc-sturm]

I will have a look at it asap

[MarvinDo]

Here is another example which possibly boils down to the same problem: The Gene DDX11L2 (ENSG00000236397) has two transcripts on two different chromosomes in NGSD: ensgid version source chromosome strand biotype ENST00000437401 1 ensembl 2 - unprocessed pseudogene ENST00000456328 2 ensembl 1 + lncRNA On the Ensembl they map to two different genes: ENSG00000236397 & ENSG00000290825

[marc-sturm]

Fixed in commit: bdd495a9473f70c1384e1345978a113e9b84a2d6

[marc-sturm]

There are still genes with transcripts on several chromosomes: ANKRD20A5P, DDX11L16, DDX11L2, LSP1P5, RPL23AP7, SNORA62, SNORA63, SNORA70, SNORA72, SNORA75, SNORD27, SNORD30, SNORD33, SNORD63, SNORD81

However they are not fixable easily, as they are caused by several Ensembl genes with the same HGNC-approved gene name, e.g.: www.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000456328 http://www.ensembl.org/Homo_sapiens/Transcript/Summary?g=ENSG00000236397;r=2:113599036-113601261;t=ENST00000437401