Sentence examples for files of libraries from inspiring English sources
To obtain the site-specific quartets of nucleotide read counts in the B6 sample, we first made mpileup files of libraries B2 and B4 using SAMtools (Li et al. 2009), then extracted the read quartets with sam2pro (http://guanine.evolbio.mpg.de/mlRho/sam2pro_0.3.tgz, last accessed May 15 , 2014, and finally combined the quartets for libraries B2 and B4.
So we first used SAMtools [ 62] to convert the.sam files of different libraries belonging to the same individual to.bam files and sort and merge them, followed by removal of potential PCR duplicates using Picard (http://broadinstitute.github.io/picard/).github.io/picard/
Additional file 1: Table of libraries, ENA accession, sequence depth and indexing sequence.
The differential RNA-seq data was generated by vertis Biotechnologie AG (Germany) as a service that included the construction of cDNA libraries before and after treatment with TAP (Additional file 1), sequencing of libraries using an Illumina HiSeq platform (single end, 50-bp read length), and the alignment of sequences to the genome (NCBI, accession number AE017283).
GenApp builds fully functioning science gateways and standalone GUI applications from collections of definition files and libraries of code fragments.
The SDF files of the studied libraries were downloaded from the vendors' websites (Additional file 1: File S1).
The raw data and processed files of the three libraries have been deposited in NCBI's Gene Expression Omnibus (GEO) [ 21, 22] under accession number GSE 17965.
Chromatogram files of the two libraries were separated into forward (5′) and reverse (3′) raw sequences, and the orientation was incorporated by a PERL script we designed.
Analysis of the readout and de novo assemblies were done with the GS FLX System Software GS De Novo Assembler (Newbler) version 2.6, using the default parameters and the "read flowgrams" (SFF files) of the shotgun library and the 3 kb paired end library as input.
b See Additional file 2a for full details of libraries and tissues.
The team of organizers worked from photographs; from Mr. Szeemann's archives (he died in 2005), which are in the Getty Institute in Los Angeles; and from documents found in the files of the Kunsthalle's library.
