README.md

In NCBI-Hackathons/SRA2R: What the package does (short line)

SRA2R

SRA2R, a package to import SRA data directly into R

This package is not maintained and is currently not functional.

SRA ToolKit examples

sra-stat example

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=sra-stat

(known good but large)
sra-stat --quick --xml SRR390728
(smaller file)
sra-stat --quick --xml SRR2971307
(small and no alignment)
sra-stat --quick --xml ERR1162649

sra-pileup

http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=sra-pileup

Command-line

sra-pileup -r chr20:1530960-1540960 SRR2971307

In R

x = read.delim(text = system('~/sratoolkit.2.5.7-ubuntu64/bin/sra-pileup -r chr20:1530960-1540960 SRR2971307',intern=TRUE))

ncbi ngs SDK details

• /usr/include/ngs (interfaces for C++ ngs)
• /usr/include/ncbi-vdb (NGS.hpp)
• /usr/local/share/doc/ngs (javadoc)
• LD_LIBRARY_PATH = /usr/local/ngs/ngs-sdk/lib64:/usr/local/ncbi/ncbi-vdb/lib64:

R and Rcpp documentation of interest

• http://dirk.eddelbuettel.com/code/rcpp/Rcpp-quickref.pdf
• http://adv-r.had.co.nz/Rcpp.html
• http://r-pkgs.had.co.nz/
• http://statr.me/rcpp-note/index.html
• https://cran.r-project.org/web/packages/Rcpp/vignettes/

NCBI-Hackathons/SRA2R documentation built on May 7, 2019, 5:18 p.m.