Scripts:
fetch: perl fetchRSEM.pl
downloads RSEM tarballs into directory 'RSEM'
extract files :
processRSEM.pl : extract normalized results files, (default used in CELLX) ( to dir LOAD )
processRSEM_exon.pl : extract the exon quantification file ( to dir EXON )
processRSEM_junction.pl : extract the junction quantification file ( to dir JUNCTION )
processRSEM_raw.pl : extract the non-normalized gene results file ( to dir RAW )
generate tables:
parseRSEM.pl
parseRSEM_exon.pl
parseRSEM_junction.pl
parseRSEM_raw.pl : raw and TPM tables
loading scripts:
loadRSEMexpression.pl
pivot tables and save as R Data obj:
makeRDataFromTableExon.pl
makeRDataFromTableJunction.pl
R Data obj for normalized RSEM and other expression level data stored in the database are generated by dumping the database contents into a file and then pivoting it into a R data obj.
datadump.pl : dump expression level data ( remove normal samples )
datadump_ALL.pl: dump all expression level data, including normal samples
makeRDataFromTableRotate.pl : pivot datadump into matrix and save as R data obj
datadumpcnv_ALL.pl : generate cnv tables
processdumpcnv.pl : post process cnv data dump to select segment of highest magnitude
makeRDataFromTableCNV.pl : generate R data obj
datadumpmut_ALL.pl : generate mutation tables
makeRDataMut.pl : generate R data obj