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The resulting reads (read length 101 bp) were processed with the Illumina BaseCaller during the sequencing step.
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Final alignment sizes larger than 200 bp were processed by a sliding-window approach with a windows size of 120 bp and a stepsize of 40 bp.
Libraries with an average insert size of ≈300 bp were processed by using the TruSeq (Illumina, Inc).
Sequencing reads of 160 bp in length were processed with Sickle (Joshi and Fass, 2011) (v1.33; available at https://github.com/najoshi/sickle) to trim both ends to remove low quality base calls.
The 50 bp CREB1 data was processed with complete genotypes, partial genotypes, and common variant information allowing 0, 1, 2 or 3 alignment mismatches.
The sequencing is processed with paired-end 101 bp reads.
Extracted fosmid DNA was processed with the Nextera DNA Sample Prep Kit (Illumina, San Diego, CA) and sequenced using Illumina MiSeq with 2 × 300 bp paired-end chemistry (Illumina, San Diego, CA).
The 1,500 bp amplicons were processed without shearing.
Short reads (36 bp or 51 bp reads) obtained were processed using Illumina Pipeline Analysis.
Reads were processed into clean 64 bp "tags" and mapped against the reference scaffolds with Bowtie 2 (ref. 58).
Samples were processed following the Illumina HTS guidelines with libraries of 200-300 bp selected via 2% agarose DNA gels.
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