Recent changes to RNA-Seq

RNA-Seq modified by Keith Ching

Keith Ching — Mon, 13 Apr 2015 18:15:46 -0000

--- v4
+++ v5
@@ -20,7 +20,27 @@
 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
+
+

RNA-Seq modified by Keith Ching

Keith Ching — Mon, 13 Apr 2015 18:07:25 -0000

--- v3
+++ v4
@@ -19,3 +19,8 @@
 parseRSEM_exon.pl
 parseRSEM_junction.pl
 parseRSEM_raw.pl : raw and TPM tables
+
+pivot tables and save as R Data obj:
+
+makeRDataFromTableExon.pl
+makeRDataFromTableJunction.pl

RNA-Seq modified by Keith Ching

Keith Ching — Mon, 13 Apr 2015 18:04:37 -0000

--- v2
+++ v3
@@ -8,7 +8,14 @@

 extract files : 

-processRSEM.pl : extract normalized results files, (default used in CELLX)
-processRSEM_exon.pl : extract the exon quantification file
-processRSEM_junction.pl : extract the junction quantification file
-processRSEM_raw.pl : extract the non-normalized gene results file
+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

RNA-Seq modified by Keith Ching

Keith Ching — Mon, 13 Apr 2015 17:57:47 -0000

--- v1
+++ v2
@@ -5,3 +5,10 @@

 downloads RSEM tarballs into directory 'RSEM'

+
+extract files : 
+
+processRSEM.pl : extract normalized results files, (default used in CELLX)
+processRSEM_exon.pl : extract the exon quantification file
+processRSEM_junction.pl : extract the junction quantification file
+processRSEM_raw.pl : extract the non-normalized gene results file

RNA-Seq modified by Keith Ching

Keith Ching — Mon, 13 Apr 2015 17:50:07 -0000

Scripts:

fetch: perl fetchRSEM.pl

downloads RSEM tarballs into directory 'RSEM'