Submitting reads

The submission of raw reads can be done programmatically, with the webinterface and using webin-cli. We will focus on the latter solution, see the referenced ENA website for other solutions.

We will need to create a manifest file, which contains the metadata for our read data and references the actual read files that should be submitted.

First, we create another directory:

mkdir -p /mnt/submission/assembly/reads

Then, we gzip the read files, since they need to be zipped for submission:

cd /mnt/WGS-data/
gzip read?.fq

And change to our submission directory:

cd /mnt/submission/assembly/reads

Create the manifest file

See this page on details for the content of the manifest file:

https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html

We just use an arbitrary number of 200 for the insert size.

We will use this short manifest template for our submission:

STUDY the accession number of your submitted study! (TODO)
SAMPLE the accession number of your submitted sample! (TODO)
NAME a_unique_experiment_name be creative! (TODO)
INSTRUMENT Illumina MiSeq
INSERT_SIZE 200
LIBRARY_SOURCE GENOMIC
LIBRARY_SELECTION RANDOM
LIBRARY_STRATEGY WGS
FASTQ path_to_fw_read_file (TODO)
FASTQ path_to_rv_read_file (TODO)

Create a file named manifest and fill it with the content above - fill the fields marked with TODO with the appropriate content. Then continue with the next step.

Validating the read submission

Before actually submitting, we are validating our manifest file. To do so, we use the option -validate in our call of webin-cli. Also, make sure, to use the -test flag to submit to the ENA test server. We also use -context=read since we are submitting reads. Other options are your -username, -password and the path to the -manifest file:

java -jar ~/webin-cli-6.10.0.jar -username=$ENA_USER -password=$ENA_PWD -context=reads -manifest=manifest -validate -test

When everything was successfully validated, you should get a message like:

INFO : The submission has been validated successfully.

Submit the reads

Now, that our read submission is validated successfully, we can go on with the submission. Just replace the -validate flag by -submit in the webin-cli call. Do NOT remove the -test flag:

java -jar ~/webin-cli-6.10.0.jar -username=$ENA_USER -password=$ENA_PWD -context=reads -manifest=manifest -submit -test

If everything works fine, you should receive a message like:

INFO : The TEST submission has been completed successfully. This was a TEST submission and no data was submitted. The following experiment accession was assigned to  the submission: ERX10008217
INFO : The TEST submission has been completed successfully. This was a TEST submission and no data was submitted. The following run accession was assigned to the submission: ERR10488906

IMPORTANT: Save the Accession of the read submission to a file, for example like this:

echo "YOUR_RUN_ACCESSION" > /mnt/submission/run.txt

Now we can go on and submit our assembly.

References

ENA - Submit Raw Reads https://ena-docs.readthedocs.io/en/latest/submit/reads.html