AICS30 MAP1LC3B-mEGFP cl22 AICS30 cl22 bam Track Settings
 
AICS30 cl22 alignment

Track collection: AICS30 MAP1LC3B-mEGFP cl22

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Source data version: July 2019
Assembly: Human Dec. 2013 (GRCh38/hg38)

AICS30 MAP1LC3B-mEGFP

Description

This track hub contains the whole exome sequences and variant calls for AICS30 MAP1LC3B-mEGFP clone 22 (public clone).

AICS30 MAP1LC3B-mEGFP

AICS30 MAP1LC3B-mEGFP is part of the Allen Cell Collection of fluorescently tagged hiPSC lines created by the Allen Institute for Cell Science. Clone 22 is publically available through Coriell. For more information on the tagged structure including live cell images visit the Allen Cell Collection and Allen Cell Explorer

Methods

Sequencing

Libraries were prepared and sequenced using the Broad Institute's Genomic Services. Exome capture was carried out using Illumina's Nextera Rapid Capture Exome Kit, and 76bp paired-end reads were generated on an Illumina HiSeq 4000.

Analysis

Adapters were trimmed using cutadapt (version 1.13). Reads were aligned to GRCh38 using bwa mem (version 0.7.13). Duplicate reads were identified using MarkDuplicates from Picard (version 2.3.0). Local realignment around indels and base quality recalibration were performed using GATK (version 3.5). Variants were called using GATK's HaplotypeCaller and hard filtered (see variants track for filtering criteria).