The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
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TLDR
SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.Abstract:
Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
Availability: http://samtools.sourceforge.net
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Citations
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Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
Gavin Ha,Gavin Ha,Andrew Roth,Andrew Roth,Daniel Lai,Ali Bashashati,Jiarui Ding,Jiarui Ding,Rodrigo Goya,Rodrigo Goya,Ryan Giuliany,Ryan Giuliany,Jamie Rosner,Arusha Oloumi,Karey Shumansky,Suet-Feung Chin,Gulisa Turashvili,Martin Hirst,Carlos Caldas,Marco A. Marra,Samuel Aparicio,Samuel Aparicio,Sohrab P. Shah,Sohrab P. Shah +23 more
TL;DR: It is shown that the majority of monoallelic expression in the transcriptomes of triple-negative breast cancer can be explained by genomic regions of LOH and an upper bound for monoalle Alic expression is established that may be explaining by other tumor-specific modifications such as epigenetics or mutations.
Journal ArticleDOI
The genomics of selection in dogs and the parallel evolution between dogs and humans
Guo-Dong Wang,Weiwei Zhai,He-Chuan Yang,He-Chuan Yang,Ruo-xi Fan,Xue Cao,Li Zhong,Lu Wang,Fei Liu,Hong Wu,Lu-Guang Cheng,Andrei D. Poyarkov,Nikolai A. Poyarkov,Shu-sheng Tang,Wenming Zhao,Yun Gao,Xue-mei Lv,David M. Irwin,David M. Irwin,Peter Savolainen,Chung-I Wu,Chung-I Wu,Ya-Ping Zhang,Ya-Ping Zhang,Ya-Ping Zhang +24 more
TL;DR: This study draws together humans and dogs in their recent genomic evolution, for the first time, and identifies a list of genes under positive selection during domestication, which overlaps extensively with the corresponding list of positively selected genes in humans.
Journal ArticleDOI
RNA-seq: technical variability and sampling
Lauren M. McIntyre,Kenneth K. Lopiano,Alison M. Morse,Victor A. Amin,Ann L. Oberg,Linda J. Young,Sergey V. Nuzhdin +6 more
TL;DR: Technical variability is too high to ignore and will persist as an issue needing to be addressed in experimental design even as the next wave of technology produces larger numbers of reads.
Journal ArticleDOI
CHCHD2 mutations in autosomal dominant late-onset Parkinson's disease: a genome-wide linkage and sequencing study
Manabu Funayama,Kenji Ohe,Kenji Ohe,Taku Amo,Norihiko Furuya,Junji Yamaguchi,Shinji Saiki,Yuanzhe Li,Kotaro Ogaki,Maya Ando,Hiroyo Yoshino,Hiroyuki Tomiyama,Kenya Nishioka,Kazuko Hasegawa,Hidemoto Saiki,Wataru Satake,Kaoru Mogushi,Ryogen Sasaki,Yasumasa Kokubo,Shigeki Kuzuhara,Tatsushi Toda,Yoshikuni Mizuno,Yasuo Uchiyama,Kinji Ohno,Nobutaka Hattori +24 more
TL;DR: CHCHD2 mutations are associated with, and might be a cause of, autosomal dominant Parkinson's disease, and further functional studies are needed to understand how mutant CHCHD 2 might play a part in the pathophysiology of Parkinson's Disease.
Journal ArticleDOI
Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells
Jonathan Göke,Xinyi Lu,Yun-Shen Chan,Huck-Hui Ng,Lam-Ha Ly,Friedrich Sachs,Friedrich Sachs,Iwona Szczerbinska,Iwona Szczerbinska +8 more
TL;DR: It is reported that repetitive elements originating from endogenous retroviruses (ERVs) are systematically transcribed during human early embryogenesis in a stage-specific manner and are a hallmark of cellular identity and cell potency that characterizes the cell populations in early human embryos.
References
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