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illuminaDataDeliveryEmail_Template.txt
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illuminaDataDeliveryEmail_Template.txt
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Subject: Sequence ready for download - sequencing run XXXXX - samples XXXX XXXX XXXX
We have now performed quality control of the sequence data for the above samples and the sequence data as well as the associated quality control files are now ready for pick-up.
------ Summary of QC results -------
The quality control files show that the sequencing data passes our error rate and quantity criteria (see one attached report example). You will therefore be billed for this service.
However, the QC report has also revealed the following features of the sample (which are most likely due to the sample preparation prior to sequencing):
XXXXXXXXXXXXXXXXX INSERT HERE: details about the QC results, for example if there are any abnormalities in base distribution or over-represented sequences XXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXX ATTACHED QUALITY CONTROL REPORT!!!!!!
XXXXXXXXXXXX TEXT TO BE USED IN CASE OF RUN FAILURE REPLACED BY ILLUMINA, ALSO CAN BE ADAPTED FOR CASE WHERE WE DO NOT MEET OUR QUANTITY OR QUALITY THRESHOLDS XXXXXXXXXXXXX
The run failed and Illumina has recognised that this is their responsibility. We will therefore be receiving replacement reagents from them. We offer you the following alternatives:
* if you are satisfied with the quality and quantity of the sequence produced, you accept this delivery. You will then be billed for any lab work we have performed (sample prep and QC) and the core facility fee.
* if you are NOT satisfied with the quality and quantity of the sequence produced, you request a "re-run" in which case you will not receive a bill until the re-run is complete, but you will then be charged the full sequencing costs and the core facility fee (in addition to any sample prep and QC costs).
------ Delivery method ------
You can pick up data by a portable hard drive (please notice the size of the data is approximately XXX GB).
You can download data and all quality control reports from NSC ftp site by applying the following information:
https://webserver1.norstore.uio.no/
username:***
password:***
You can extract *.tar file by typing the following command in the terminal:
tar -xvf *.tar
A md5sum.txt file is included in the result folder. In the folder, you can check whether the files are downloaded completely by type the following command in the terminal:
md5sum -c md5sum.txt
If all the fastq.gz files are OK, you should see OK after each file name, e.g.:
.//Sample_A/A_CAGATC_L002_R1_001.fastq.gz: OK
You haven't specify delivery method for these data in sample submission form. Please specify whether your samples are human samples (not including samples from human cell lines) and the method you want us to deliver data.
You can choose one of the following way:
1, Portable hard drive to be picked-up from UllevŒl by user. You may choose whether you wish to deliver your own portable hard drive to NSC or whether NSC should purchase a portable hard drive for you (you will charged for this at approx. 1,000 NOK per TB).
2, Upload to NSC ftp site (we will send you the address, a username and password).
3, Upload to customer ftp site (please provide address, username and password to be used by NSC)
4, Upload to norstore or titan (option only available for non-human samples and for users with accounts on these systems). Please provide location (path), ensure it is possible for NSC to write to this location and that there is sufficient free quota.
5, Portable storage device (memory stick or DVD depending on capacity required).
Or we can discuss other ways. Please note, based on security reason, if your samples are human samples (not including samples from human cell lines), you can only choose method 1 or 5.
------ Data security ------
If this sequence data relates to human samples, you are responsible for storing it in a way that complies with the local jurisdiction.
------ Data storage policy (updated on May 1, 2013) -------
Data will be stored at our local storage facility for a period of 3 months from the date of the delivery mail after which it will be permanently deleted. A reminder notice will be sent to the contact email address two weeks prior to deletion.
------ Understanding the data ------
Here is an overview of your data files and the number of fragments that were sequenced. Samples are identifiable through the file names: file name consists of sampleName_index_lane_read_digit.fastq.gz:
XXXXXXXXXXXXXXXX sample to lane mapping with fragment numbers XXXXXXXXXXXXXXXXXXXXX
Use the following formula to compute the yield (in number of bases): number of reads x read length (note: for pair-end sequencing, there are two fastq files associated with one sample)
Please refer to our website (http://www.sequencing.uio.no/services/data-delivery/) for a detailed explanation of file contents and formats. This web page contains a lot of information that is essential to understanding your sequence data, so please read it. However, we would like to particularly emphasize one very IMPORTANT point: the sequence files are in Sanger fastq format (see http://en.wikipedia.org/wiki/FASTQ_format).
----- Alignment -----
The alignment of the reads to a reference genome is not a deliverable from the NSC, but we will perform it for users that request it. If you wish for such an alignment to be performed please inform us of which version of the reference genome you wish your sequences to be aligned to.
----- Further bioinformatic analyses ----
Beyond the alignment to a reference, the NSC does not provide bioinformatic services. We are willing to advise on general issues, but, if the help requested involves having to invest time into getting to understand specifics of a user project or actually performing analyses for the user, then the terms on which this help will be provided will need to be discussed. In general, such help, if provided, will take the form of a collaboration with the user or of a paid service.
------- Acknowledgement -------
The Norwegian Sequencing Centre (NSC) operates as a core facility and you will therefore not be billed for the labour costs incurred. However, you are requested to acknowledge the support you have received from the bodies funding the NSC. Please use the following text in articles or reports relating to this sequence data:
"The sequencing service was provided by the Norwegian Sequencing Centre (www.sequencing.uio.no), a national technology platform hosted by the University of Oslo and supported by the "Functional Genomics" and "Infrastructure" programs of the Research Council of Norway and the Southeastern Regional Health Authorities".
----- Conclusion ------
Please let us know how you get on with the above. It is not unlikely that you experience some problem (or have a question), in which case don't hesitate to get in touch. Hopefully, however, everything is fine and you are able to download, access and understand your data, in which case we also value your feedback.