Merge pull request #7 from Blahah/patch-2

Remove obsolete RPKM from output documentation

doc/source/salmon.rst

@@ -233,9 +233,9 @@ with a ``#`` is a comment line, and can be safely ignored.  Salmon records the f
 and options passed to it in comments at the top of its output file.  The last comment 
 line gives the names of each of the data columns. The columns appear in the following order: 
 
-+------+--------+-----+------+----------+
-| Name | Length | TPM | FPKM | NumReads |
-+------+--------+-----+------+----------+
++------+--------+-----+----------+
+| Name | Length | TPM | NumReads |
++------+--------+-----+----------+
 
 Each subsequent row described a single quantification record.  The columns have
 the following interpretation.
@@ -250,12 +250,6 @@ the following interpretation.
   This is salmon's estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM).
   TPM is the recommended relative abundance measure to use for downstream analysis. 
 
-* **FPKM** ---
-  This is salmon's estimate of the relative abundance of this transcript in units of Fragments Per Kilobase per Million
-  mapped reads (FPKM).  This relative abundance measure is proportional, within-sample, to the TPM measure.  However, 
-  the TPM should generally be preferred to FPKM.  This column is provided mostly for compatibility with tools that expect
-  FPKM as input.
-
 * **NumReads** --- 
   This is salmon's estimate of the number of reads mapping to each transcript that was quantified.  It is an "estimate" 
   insofar as it is the expected number of reads that have originated from each transcript given the structure of the uniquely