=================================== Submitting Transcriptome Assemblies =================================== - `Introduction`_ - `Stage 1: Pre-register study and sample`_ - `Stage 2: Prepare the files`_ - `Stage 3: Validate and submit the files`_ - `Assigned accession numbers`_ - `Validation rules`_ Introduction ============ Transcriptome assemblies can be submitted to the European Nucleotide Archive (ENA) using the `Webin command line submission interface <../general-guide/webin-cli.html>`_ with ``-context transcriptome`` option. A transcriptome assembly consists of: - General assembly information - Study accession or unique name (alias) - Sample accession or unique name (alias) - Assembly name - Assembly program - Sequencing platform - Free text description of the transcriptome assembly (optional) - Sequences - Functional annotation (optional) The below image illustrates the stages of the transcriptome assembly submission process: .. image:: ../images/webin-cli_01.png Stage 1: Pre-register study and sample ====================================== Each submission must be associated with a pre-registered study and a sample. For transcriptomic assemblies, raw reads must also be submitted to give context to the data. - `Register a Study <../study.html>`_ - `Register a Sample <../samples.html>`_ - `Submit Read Data <../reads.html>`_ Stage 2: Prepare the files ========================== The set of files that are part of the submission are specified using a manifest file. The manifest file is specified using the ``-manifest `` option. A transcriptome assembly submission consists of the following files: - 1 manifest file - 1 FASTA file OR 1 `flat file <../fileprep/assembly.html#flat-file>`_ Transcriptome assemblies should be of a high enough quality to fulfil the following criteria: 1. They must have at least 1x coverage by primary sequence at each base. Regions of a TSA record can be assembled from a single Expressed Sequence Tag (EST) or read so that coverage is only 1x. 2. Bases that are listed as 'n' should be less than 10%. 3. They should not have a stretch of more than 15 n's in a row. If they are within 20 base pairs of the c- or n-terminus they should be removed. 4. No assemblies can be shorter than 200 base pairs. 5. Any vector sequence or primers should be removed. Manifest file ------------- The manifest file has two columns separated by a tab (or any whitespace characters): - Field name (first column): case insensitive field name - Field value (second column): field value The following metadata fields are supported in the manifest file: - STUDY: Study accession or unique name (alias) - SAMPLE: Sample accession or unique name (alias) - ASSEMBLYNAME: The unique assembly name - ASSEMBLY_TYPE: 'isolate' - PROGRAM: The assembly program - PLATFORM: The sequencing platform, or comma-separated list of platforms - DESCRIPTION: Free text description of the transcriptome assembly (optional) - RUN_REF: Comma separated list of run accession(s) (optional) The following file name fields are supported in the manifest file: - FASTA: sequences in FASTA format - FLATFILE: sequences in `EMBL-Bank flat file format <../fileprep/flat-file-example.html>`_ For example, the following manifest file represents a genome assembly consisting of transcripts provided in one FASTA file: :: STUDY TODO SAMPLE TODO ASSEMBLYNAME TODO ASSEMBLY_TYPE isolate PROGRAM TODO PLATFORM TODO FASTA transcriptome.fasta.gz Fasta file ---------- Unannotated sequences should be submitted as a Fasta file. The sequence name is extracted from the fasta header. For example the following header contains the name 'contig1': `>contig1` Flat file --------- Annotated sequences must be submitted using an EMBL-Bank flat file. The sequence name is extracted from the AC * line and must be prefixed with a '_'. For example the following AC * line defines name 'contig1': `AC * _contig1` Stage 3: Validate and submit the files ====================================== Files are validated, uploaded and submitted using the `Webin command line submission interface (Webin-CLI) <../general-guide/webin-cli.html>`_. Please refer to the `Webin command line submission interface <../general-guide/webin-cli.html>`_ documentation for more information about the submission process. Assigned accession numbers ========================== Once the genome assembly has been submitted an analysis (ERZxxxxxx) accession number is immediately assigned and returned to the submitter by the Webin command line submission interface (Webin-CLI). ERZ accessions **should not** be used to reference the assembly in publications. The purpose of the ERZ accession number is for the submitter to be able to refer to their submission within the Webin submission service. For example, the submitter can retrieve the assigned sequence accessions from the `Webin Portal <../general-guide/submissions-portal.html>`_ or from the `Webin reports service <../general-guide/reports-service.html>`_ using the ERZ accession number. Sequence accessions are sent to the user by email once the TSA has completed processing. The ERZ accession should be used to refer to the assembly in any conversations with helpdesk staff. For transcriptome assemblies, long term stable accession numbers that can be used in publications are: - Study accession (PRJEBxxxxxx) assigned at time of study registration - Sample accession (SAMEAxxxxxx) assigned at time of study registration - Sequence accession(s) assigned once the genome assembly submission has been fully processed by ENA See an example of a publicly available TSA at: https://www.ebi.ac.uk/ena/browser/view/GAAJ01000000 Validation rules ================ Sequence validation rules ------------------------- Sequences must: - have unique names within an assembly - be at least 200bp long - not have terminal Ns - consist of bases: 'a','c','g','t','u','b','d','h','k','m','n','r','s','v','w','y'