alias: 2 puregene
title: human cerebellum puregene extraction
design: Library construction was undertaken using TruSeq DNA PCR Free chemistry (Illumina Inc., San Diego, CA)  to prepare dual indexed, paired-end libraries from 2 micrograms of genomic DNA, according to standard protocols supplied by Illumina (Illumina Inc., San Diego, CA) The DNA libraries were sequenced, 2x101 bases in one lane of a Rapid Run flowcell on a HiSeq2500 sequencing system (Illumina, Inc., San Diego, CA) Prior to alignment, Illumina data (fastq) is trimmed of Illumina adapters and soft clipped to remove the low-quality bases at the end of the read (Q>10). Picard tools (FastqToSam) was used to convert the fastq files to unaligned BAM files. Reads were then aligned to the hg19 reference genome using Novoalign (v3.02.002), including base score quality recalibration. The generated aligned .bam files were then sorted in coordinate order using Picard tools. .bam files are fed into GATK for local realignment around Indels. We also marked/removed PCR duplicated with Picard tools. Coverage and GC bias metrics were calculated with Picard tools.
identifiers.namespace: University College London
identifiers.id: 2 puregene