[ensembl-dev] Access to RNAseq samples used for gene annotation
thibaut at ebi.ac.uk
Mon Aug 15 10:31:04 BST 2022
We don’t have a simple list of the samples that we used. But you can retrieve this information from the FTP.
To get the list of the names of the samples, you can either look in the README which will have the list or you can look at the name of the BAM files, they are in the format <assembly name>.<provider>.<sample name>.<version>.bam
From the BAM files you can retrieve the sample accession(s) for the “sample”. When there is multiple accession for the same tissue name, we merge the data.
For the current annotation on GRCg7b, these files are not yet available on the FTP and you will need to wait for release 108. However we use the same set that was used for the latest GRCg6a annotation with the addition of the data from the GENE-SWitCH project.
> On 12 Aug 2022, at 18:47, Fabien Degalez <fabien.degalez at inrae.fr> wrote:
> Hi everyone,
> I would like to know if it's possible to have access to the list of RNA-seq samples used for the gene annotation (more precisely for the chicken one, even if i think that is the same for all the others).
> Indeed, on the PDF linked to gene annotation, it just says that "samples from ENA were used" but without any more precision.
> I don't know if I should use the API or if the information is on the website or on the FTP server.
> Thank you for your help.
> Fabien DEGALEZ
> Fabien DEGALEZ
> Doctorant en génétique, génomique et bio-informatique
> UMR 1348 PEGASE, INRAE – Institut Agro, Agrocampus Ouest Rennes
> Équipe Génétique & Génomique
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