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== Reads sampling and trimming == * Randomly sample 1000 reads from the following libraries for analysis: 1. Blueprint samples #1 and #2 from the Aug 28 MiSeq run. (compare different BP samples) - BP1, BP2 2. Technical replicates for Blueprint samples #1 and #2 from the Aug 28 MiSeq run. (compare different captures) - BP1rep, BP2rep 3. Technical replicates for Blueprint samples #1 and #2 from the Sep 13 HiSeq Rapid run. (compare different runs) - BP1rep-hiseq, BP2rep-hiseq 4. NA12878 captured with the original probes set and sequenced in HL157 (+ control) - HMrep1 5. NA12878 captured with the normalized probes set and sequenced in HL157 (+ control) - HMrep2 6. NA12878 captured with the normalized probes set and sequenced in HiSeq Rapid run - HMrep3 7. DMR330K capture from the Mar22 MiSeq run as positive control. (+ control) - H1-dmr330k 8. NA12878 captured with the original probes set and sequenced in June 20 MiSeq run (+ control) - HM-Miseq1, HM-Miseq2 * All reads were sampled from only read 1. * Sampling was done randomly by using "sort -R" and then taking the first 1000 reads after random sorting. * All reads were trimmed 27 bp from the 5' end and quality trimmed using mean quality score of 30.
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