CONTENT ------- This folder contains the targeted, next generation sequencing data from a primary breast cancer and associated metastatic lymph node, which was analyzed in the following paper: Zare, Habil, Junfeng Wang, Alex Hu, Kris Weber, Josh Smith, Debbie Nickerson, ChaoZhong Song, Daniela Witten, C. Anthony Blau, and William Stafford Noble. "Inferring clonal composition from multiple sections of a breast cancer." PLoS computational biology 10, no. 7 (2014): e1003703. SUBSECTIONS ----------- 13 subsections were sequenced including 10 primary tumor subsections, 2 subsections from a metastatic lymph node, and 1 normal sample. Each file name has the following form: -_*_fastq.gz For each subsection, 2 replicates were sequenced which are denoted by ii and iii in the file names. The following table shows how the fastq files can be matched by the subsection names as referred in the above paper. Subsection-ID (in file name) Reference ID (in paper) Source ------------------------------------------------------------------ A5-2 N1-1 normal A1-1 P1-1 primary A1-2 P1-4 primary A1-3 P1-3 primary A1-4 P1-2 primary A2-1 P3-1 primary A2-3 P3-2 primary A3-1 P2-1 primary A3-2 P2-2 primary A3-3 P2-3 primary A3-4 P2-4 primary B1-1 M1-2 metastatic B1-2 M1-1 metastatic MORE DETAILS ------------ For further information, please refer to the paper, and feel free to contact a corresponding author of the paper if you have any questions. This readme file was created by Habil Zare on 9 Nov 2014.