v1.1.5.b

diff --git a/README.md b/README.md
index b95c4ea51cffc471d5b211ab84fc07aabeeb0e64..0f96f6993d0c38e3a923bae9746849555f42f7c8 100644 (file)
--- a/README.md
+++ b/README.md
@@ -136,10 +136,18 @@ outF: the file name for plots generated from the model. It is a pdf file
 
 The plots generated depends on read type and user configuration. It
 may include fragment length distribution, mate length distribution,
 
 The plots generated depends on read type and user configuration. It
 may include fragment length distribution, mate length distribution,

-read start position distribution (RSPD), quality score vs percentage
-of sequecing error given the reference base, position vs percentage of
-sequencing error given the reference base.
+read start position distribution (RSPD), quality score vs observed
+quality given a reference base, position vs percentage of sequencing
+error given a reference base.

 
 

+fragment length distribution and mate length distribution: x-axis is fragment/mate length, y axis is the probability of generating a fragment/mate with the associated length
+
+RSPD: Read Start Position Distribution. x-axis is bin number, y-axis is the probability of each bin. RSPD can be used as an indicator of 3' bias
+
+Quality score vs. observed quality given a reference base: x-axis is Phred quality scores associated with data, y-axis is the "observed quality", Phred quality scores learned by RSEM from the data. Q = -10log_10(P), where Q is Phred quality score and P is the probability of sequencing error for a particular base
+
+Position vs. percentage sequencing error given a reference base: x-axis is position and y-axis is percentage sequencing error
+ 

 ## <a name="example"></a> Example
 
 Suppose we download the mouse genome from UCSC Genome Browser.  We will
 ## <a name="example"></a> Example
 
 Suppose we download the mouse genome from UCSC Genome Browser.  We will

diff --git a/calcCI.cpp b/calcCI.cpp
index d1f26e56bb8802e42a531fd795a2e7a5818b8d10..321cd4ac7e5319ea4b98998c6ab0d24cd1a5d271 100644 (file)
--- a/calcCI.cpp
+++ b/calcCI.cpp
@@ -378,7 +378,7 @@ int main(int argc, char* argv[]) {
 
        delete[] tau_denoms;
 
 
        delete[] tau_denoms;
 

-       sprintf(command, "rm -f %s", tmpF);
+               sprintf(command, "rm -f %s", tmpF);

        int status = system(command);
        if (status != 0) {
          fprintf(stderr, "Cannot delete %s!\n", tmpF);
        int status = system(command);
        if (status != 0) {
          fprintf(stderr, "Cannot delete %s!\n", tmpF);

diff --git a/rsem-plot-model b/rsem-plot-model
index c0eaa1b0b70faa4175478830b8e5d26fd4eff61c..333a9e7b2e9b2ba1371f06f56e52d3b6cbbf6a87 100755 (executable)
--- a/rsem-plot-model
+++ b/rsem-plot-model
@@ -96,10 +96,10 @@ if (model_type == 1 || model_type == 3) {
     vecG <- as.numeric(list[[3]])
     vecT <- as.numeric(list[[4]])
     if (sum(c(vecA, vecC, vecG, vecT)) < 1e-8) break
     vecG <- as.numeric(list[[3]])
     vecT <- as.numeric(list[[4]])
     if (sum(c(vecA, vecC, vecG, vecT)) < 1e-8) break

-    peA <- c(peA, ifelse(sum(vec) < 1e-8, NA, 1.0 - vecA[1]))
-    peC <- c(peC, ifelse(sum(vec) < 1e-8, NA, 1.0 - vecC[2]))
-    peG <- c(peG, ifelse(sum(vec) < 1e-8, NA, 1.0 - vecG[3]))
-    peT <- c(peT, ifelse(sum(vec) < 1e-8, NA, 1.0 - vecT[4]))
+    peA <- c(peA, ifelse(sum(vec) < 1e-8, NA, (1.0 - vecA[1]) * 100))
+    peC <- c(peC, ifelse(sum(vec) < 1e-8, NA, (1.0 - vecC[2]) * 100))
+    peG <- c(peG, ifelse(sum(vec) < 1e-8, NA, (1.0 - vecG[3]) * 100))
+    peT <- c(peT, ifelse(sum(vec) < 1e-8, NA, (1.0 - vecT[4]) * 100))

   }
 
   x <- 1 : length(peA)
   }
 
   x <- 1 : length(peA)