RNA-Seq

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