Project Report

M.Dopson_17_06_project_summary

2018

Project Information

User Project Name

sysmetex_leaching_manuscript_LNU_samples

NGI Project Name

M.Dopson_17_06

NGI Project ID

P9658

NGI Facility

Genomics Production Stockholm

User Contact

NGI Application Type

RNA-seq (no best practice analysis)

Submitted samples

12 samples

Ordered lanes

2.0 lanes

Order Dates

Order received: 2017-12-04, Contract received: 2017-12-14, Samples received: 2017-12-14, Report date: 2018-04-12

Reference Genome

(Multiple (-, -))

Report generated by

Jun Wang, 2018-04-12

Swedac Accreditation

The National Genomics Infrastructure is accredited by Swedac. This means that our services are subject to highly stringent quality control procedures, so that you can be sure that your data is of excellent quality.

Methods

Library construction

Sequencing

  1. Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 2x126 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using bcl2fastq_v2.19.1.403 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.

Data Flow

Raw sequencing data is demultiplexed and converted to FastQ on site before being transferred securely to UPPMAX for delivery.

Data Processing

To ensure that all sequenced data meets our guarantee of data quality and quantity, a number of standardised bioinformatics quality control checks are performed before delivery. These include checking the yield, sequence read quality and cross-sample contamination.

Accredited workflow

Library preparation

Validated under ISO accreditation 17025:2005

Sequencing

Validated under ISO accreditation 17025:2005

Data Processing

Validated under ISO accreditation 17025:2005

Data Analysis

Not Applicable

Sample Information

Sample information table can be viewed tab-separated text file, please click here (table hidden due to number of samples). Below you can find an explanation of the header column used in the table.

Library Information

Library information table can be viewed tab-separated text file, please click here (table hidden due to number of samples). Below you can find an explanation of the header column used in the table.

Lanes Information

Date Flowcell Lane Clusters(M) PhiX >=Q30(%) Method
180406 ACBKUTANXX 3 287 0.39 89.34 A
180406 ACBKUTANXX 4 288 0.4 89.43 A

The table is also saved as parseable tab-separated text file for convenience. Below you can find an explanation of the header column used in the table.

General Information

Naming conventions

The data is delivered in FastQ format using Illumina 1.8 quality scores. There will be one file for the forward reads and one file for the reverse reads (if the run was a paired-end run).

The naming of the files follow the convention:

[NGI-NAME]_[BCL-CONVERSION-ID]_[LANE]_[READ]_[VOLUME].fastq.gz

Data access at UPPMAX

Data from the sequencing have been be uploaded to the UPPNEX (UPPMAX Next Generation sequence Cluster Storage, uppmax.uu.se) called GRUS. More details can be found on the following links

Acknowledgements

In publications based on data from the work covered by this agreement, the authors must acknowledge SciLifeLab, NGI and Uppmax:

The authors would like to acknowledge support from Science for Life Laboratory, the National Genomics Infrastructure, NGI, and Uppmax for providing assistance in massive parallel sequencing and computational infrastructure.

Further Help

If you have any queries, please get in touch at .