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illuminaDataDeliveryEmail_Example.txt
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illuminaDataDeliveryEmail_Example.txt
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Subject:Sequence ready for download - sequencing run 141107_D00399_0034_BC5V1RANXX - Project_RAD-AnneB-141107
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.
----- Delivery method ------
You can download data and all quality control reports from NSC ftp site by applying the following information:
http://webadress
username: username
password: password
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
------ 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:
RAD3-Coch_NoIndex_L004_R1_001.fastq.gz 188,092,565 fragments
RAD3-Coch_NoIndex_L004_R2_001.fastq.gz 188,092,565 fragments
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.
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