From 4f3469e2d5395526c0376688ded4340a4834677d Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Fri, 17 Jul 2020 11:42:15 +0100 Subject: Started EBI submission --- doc/blog/using-covid-19-pubseq-part6.org | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) (limited to 'doc/blog') diff --git a/doc/blog/using-covid-19-pubseq-part6.org b/doc/blog/using-covid-19-pubseq-part6.org index 2a7c593..2d1c5e0 100644 --- a/doc/blog/using-covid-19-pubseq-part6.org +++ b/doc/blog/using-covid-19-pubseq-part6.org @@ -23,7 +23,10 @@ why not export the same to EBI too with the least amount of effort? COVID-19 PubSeq is a data source - both sequence data and metadata - that can be used to push data to other sources, such as EBI. You can -register [[https://ena-docs.readthedocs.io/en/latest/submit/samples/programmatic.html][samples programmatically]] with a specific XML interface. +register [[https://ena-docs.readthedocs.io/en/latest/submit/samples/programmatic.html][samples programmatically]] with a specific XML interface. Note +that (at this point) if you want to submit a sequence (FASTA) it can +only be done through the [[https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html][Webin-CLI]]. Raw data (FASTQ) can go through +the XML interface. EBI sequence resources are presented through ENA. For example [[https://www.ebi.ac.uk/ena/browser/view/MT394864][Sequence: MT394864.1]]. @@ -42,9 +45,9 @@ EBI has XML Formats for - PROJECT with the schemas listed [[ftp://ftp.ebi.ac.uk/pub/databases/ena/doc/xsd/sra_1_5/][here]]. Since we are submitting sequences we -should follow submitting [[https://ena-docs.readthedocs.io/en/latest/submit/assembly.html][full genome assembly guidelines]] and [[https://ena-docs.readthedocs.io/en/latest/submit/general-guide/programmatic.html][ENA -guidelines]]. The first step is to define the study, next the sample and -finally the sequence (assembly). +should follow submitting [[https://ena-docs.readthedocs.io/en/latest/submit/assembly.html][full genome assembly guidelines]] and +[[https://ena-docs.readthedocs.io/en/latest/submit/general-guide/programmatic.html][ENA guidelines]]. The first step is to define the study, next the sample +and finally the sequence (assembly). * Defining the EBI study -- cgit v1.2.3