SRA2R, a package to import SRA data directly into R
This package is not maintained and is currently not functional.
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
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))
- /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: