Sandbox dataset for testing

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Sandbox datasets for testing

  • We have decided to have sandbox datasets of 5 and 24 samples sequenced in Geneva for testing purposes
  • See the attached files for the sample IDs and fastq filenames
  • All these fastq files can be found from /upload/geuvadis/wp4_rnaseq/main_project/sequence_data/fastq/mrna
  • These files have been mapped to hg19 with bwa in Geneva. If you want to use the resulting bam files for something (e.g. testing for genomic contamination), they are in /upload/geuvadis/wp4_rnaseq/main_project/working/mapping/bam/normal_hg19/bwa
  • The 5 samples are the same 5 that have been done in replicate in all the labs, but please use the fastq files from Geneva for methods testing. These data has been checked to be of good quality and pretty much average in terms of coverage, except for HG00117 that has the highest coverage of all the 103 of the first sequencing batch in Geneva.
  • The 24 samples include the 5 and 19 randomly selected other samples. Tuuli has done basic QC to see that coverage is adequate and there are no major outliers.

File:Sandbox5 fastq.txt
File:Sandbox24 fastq.txt

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