FAQ
Which taxid should I use for environmental samples?
Can I upload my read data files and XML into my drop box?
Which compression formats do you accept for Fastq files?
Can I submit multiplexed read data? If not, how do I demultiplex?
I tried to upload my files using FTP but failed because of '553 Could not create file' error. What should I do?How can I edit my submitted records?
How do I search for all RNA-Seq experiments from bovine samples?
General
What is ENA?
The European Nucleotide Archive (ENA) provides a comprehensive record of the world's nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. More information about ENA is available here.
What is SRA?
The Sequence Read Archive (SRA) is part of ENA that provides a repository for sequence read and analysis data (such as alignments and variation calls).
Taxonomy
How do I request a new taxid?
Data submitted to ENA is associated directly, or indirectly via samples, to taxids. Please contact datasubs@ebi.ac.uk to request for taxids for newly sequenced organisms.
Which taxid should I use for environmental samples?
Environmental samples, to which sequencing is applied without isolation of individual species or strains from the sample, are labelled in ENA with one of a range of 'environmental sequence' taxids, that relate to the sampling environment rather than to a conventional taxonomic grouping. The list of these taxids is available in the 'Navigation' tab from the following ENA Browser page:
http://www.ebi.ac.uk/ena/data/view/Taxon:408169
Or as a result from the ENA Advanced Search.
Which taxid should I use for a mixed community of organisms (e.g. for 16S rRNA sequencing)?
All samples of mixed communities for the purposes of metagenomics, metatranscriptomics, diversity analysis, etc., must use environmental taxids. Please refer to the previous answer for instructions on how to obtain the list of environmental taxids.
Submissions
Can I upload my read data files and XML into my drop box?
The submission process consists of two steps. First you need to upload your data files only into your drop box. After this metadata is submitted interactively using SRA Webin or programmatically using SRA Rest. More information about submissions is available here.
Which compression formats do you accept for Fastq files?
We only accept GZIP and BZIP2 compression formats. Especially we don't accept 7-ZIP or TAR compressed files. More information about supported Fastq file formats is available here.
Can I submit multiplexed read data? If not, how do I demultiplex?
ENA does not currently accept multiplexed data. Submitted data files must only contain reads from a single sample. Demultiplexing can be done using tools such as sfffile.
Further instructions for demultiplexing sff files is available here.
I tried to upload my files using FTP but failed because of '553 Could not create file' error. What should I do?
Most command line FTP clients use passive FTP data transfer that may be blocked by local firewalls in their default configurations. Other FTP clients, such as FileZilla, use active FTP data channels, which are by default allowed by firewalls.
Please contact your local systems administrator to allow passive FTP data transfers or use an FTP client that supports active FTP data tranfer. Instructions on using FileZilla to upload data are available here.
How can I edit my submitted records?
You can edit your records using SRA Webin.
Search
How do I search for all RNA-Seq experiments from bovine samples?
- Go to the Advanced Search in the ENA Browser
- Select 'Read' domain
- In the 'Taxon name' field, enter: Bos taurus
- In the 'Library strategy' field, select: RNA-Seq