From 9d31ca4ec61cab10001f08f86486ef7451456989 Mon Sep 17 00:00:00 2001 From: alisha246 Date: Thu, 30 Nov 2023 09:43:34 +0000 Subject: [PATCH 1/2] flat file link correct flat file link --- retrieval/ena-analysis.rst | 18 +++++++++++++++++- submit/sequence.rst | 2 +- 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/retrieval/ena-analysis.rst b/retrieval/ena-analysis.rst index e8c96f2b..8bb38ea5 100644 --- a/retrieval/ena-analysis.rst +++ b/retrieval/ena-analysis.rst @@ -71,4 +71,20 @@ If there are chromosomes in the assembly, they can be viewed through the assembl The ‘Assembly Statistics’ shows all details of the assembly being viewed. .. image:: images/assembly-statistics.png - :align: center \ No newline at end of file + :align: center + +View and Download Files +----------------------- + +This section explains how to view and download assembly and sequence files from the ENA browser. This only applies to +publicly available data. The ‘View’ option displays and the ‘Download’ option downloads the files that are being +accessed. For example, the options shown in the navigation box below have the following functions: + +- **XML** - Displays/downloads the file containing all the assembly attributes displayed in XML format. +- **WGS Set EMBL** - If an assembly contains contigs, downloads the assembly’s WGS contig set in embl (flat file) + format. +- **WGS Set FASTA** - If an assembly contains contigs, downloads the assembly’s WGS contig set in fasta format. +- **All Seq EMBL** - Downloads all sequences in the assembly including all contigs, scaffolds and chromosomes as + applicable in embl (flat file) format. +- **All Seq FASTA** - Downloads all sequences in the assembly including all contigs, scaffolds and chromosomes as + applicable in fasta format. diff --git a/submit/sequence.rst b/submit/sequence.rst index 206850fe..f70b1541 100644 --- a/submit/sequence.rst +++ b/submit/sequence.rst @@ -70,7 +70,7 @@ Submission Options There are two ways in which targeted sequences can be submitted: all targeted sequences can be submitted in the -`EMBL flat file format `_. +`EMBL flat file format `_. Alternatively, for commonly submitted types of sequence there are checklists which can be used for submission instead. In checklist-based submission, you provide a spreadsheet of pre-defined attributes for each sequence, and our pipeline automatically creates flat files based on these. From 65dc04c7f31194638dc1591c5c70991cce22b33d Mon Sep 17 00:00:00 2001 From: alisha246 Date: Wed, 4 Dec 2024 14:25:23 +0000 Subject: [PATCH 2/2] add link added link --- update/metadata/interactive.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/update/metadata/interactive.rst b/update/metadata/interactive.rst index d6a9900e..c0f8fc82 100644 --- a/update/metadata/interactive.rst +++ b/update/metadata/interactive.rst @@ -24,7 +24,7 @@ For samples, there may sometimes be good reason to add, remove, or edit the elem - 1: `Study Edits`_ - 2: `Sample Edits`_ - 3: `Experiment And Run Edits`_ -- 4: `Analysis Edits` +- 4: `Analysis Edits`_ Study Edits