For a current project I'm analyzing human whole exome sequencing data prepared with the nextera rapid capture expanded exome kit. Our own data were generated using a "non-standard" workflow and I would like to compare capture efficiency, etc. with existing data prepared with the same kit.
Available data which are based on this kit, however, seem to be extremely scarce. So far, I was only able to find one bioproject (PRJNA268172) in the SRA and DDBJ which explicitly names this kit. Unfortunately, I found the sequences in the project very "weird" (reads are all 5' and 3' clipped for unknown reasons, Phred score distributions look strangely even and interleaved reads are sequentially numbered and subsequent reads doesn't seem to belong together) and I'm therefore looking for other projects.
I have currently contacted two authors who described the use of the kit in their publication (unfortunately, no reference to a data deposition is given or I'm unable to see it...), but - while waiting for a response - I'm looking for additional/other data. Any help will be greatly appreciated.
Dear Stefano,
Thanks for the fast reply. After looking through your attachments, I have to say that this is not what I'm looking for.
Maybe, I should have stated more clearly, that I do know how to analyze the data and what the quality metrics, specifications and underlying principles of the nextera kits are. However, I do need "real sequencing data", i.e. fastq files from a sequenced capture library prepared with the nextera expanded exome kit. Preferably, I'm looking for data not derived from cell lines but for now, everything is fine.
Best,
Urs
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