doc update

modules/bamutils/count/index.md

@@ -13,13 +13,13 @@ module: bamutils
 
     [gtf]
         Calculate the number of reads that map within the coding regions of each
-        gene. If [-norm] is given, an RPKM calculation is also performed,
-        yielding the normalized RPKM value for each gene.
+        gene. If [-norm] is given, an FPKM calculation is also performed,
+        yielding the normalized FPKM value for each gene.
 
         For paired-end reads, each read will only count once for each gene.
 
         Requires: GTF file
-        Calculates: # reads, RPKM, coverage
+        Calculates: # reads, FPKM, coverage
 
 
     [exon]
@@ -37,7 +37,7 @@ module: bamutils
 
         Requires: GTF file
         Calculates: # reads,
-                    RPKM,
+                    FPKM,
                     # const region reads for gene,
                     # region reads,
                     # region excluding reads (spliced out),
@@ -66,7 +66,7 @@ module: bamutils
         in a BED6 formated file: chrom, start (0-based), end, name, score, strand.
 
         Requires: BED file
-        Calculates: # reads, RPKM, coverage
+        Calculates: # reads, FPKM, coverage
 
 
     [repeat]
@@ -75,15 +75,15 @@ module: bamutils
         Output is the number of reads that map to each repeat element.
 
         Requires: RepeatMasker file
-        Calculates: # reads, RPKM
+        Calculates: # reads, FPKM
 
     [repeatfam]
         Calculates the number of reads that map to various repeat regions in the
         genome.  Repeat regions are defined by annotations from repeatmasker.org.
         Output is the number of reads that map to each family/member of repeats.
 
         Requires: RepeatMasker file
-        Calculates: # reads, RPKM
+        Calculates: # reads, FPKM
 
     [bin]
         Calculates the number of reads in bins of N bases. Reads
@@ -115,7 +115,7 @@ module: bamutils
         -uniq              only count unique starting positions
                            (avoids possible PCR artifacts, not recommended)
         -startonly         Only take into account the start pos of the read to assign counts
-        -rpkm              calculate RPKM values based on millions of mapped reads
+        -fpkm              calculate FPKM values based on millions of mapped reads
                            and the length of the region in kb (number of mapped reads
                            determined by -norm value)
         -norm <value>      how to normalize counts

modules/bamutils/index.md

@@ -8,7 +8,7 @@ module: bamutils
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/minorallele">minorallele</a></td><td>Find potential minor allele frequency (experimental)</td></tr>
 <tr><td colspan="3"><h3>RNA-seq</h3></td></tr>
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/cims">cims</a></td><td>Finds regions of unusual deletions (CLIP-seq) (experimental)</td></tr>
-<tr><td>&nbsp;</td><td><a href="/modules/bamutils/count">count</a></td><td>Calculates counts/RPKM for genes/BED regions/repeats (also CNV)</td></tr>
+<tr><td>&nbsp;</td><td><a href="/modules/bamutils/count">count</a></td><td>Calculates counts/FPKM for genes/BED regions/repeats (also CNV)</td></tr>
 <tr><td colspan="3"><h3>General</h3></td></tr>
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/convertregion">convertregion</a></td><td>Converts region mapping to genomic mapping</td></tr>
 <tr><td>&nbsp;</td><td><a href="/modules/bamutils/export">export</a></td><td>Export reads, mapped positions, and other tags</td></tr>

modules/fastqutils/unmerge/index.md

@@ -9,7 +9,7 @@ module: fastqutils
     Files will be written as "out_template.N.fastq" where N is the
     pair number.
 
-    Usage: fastqutils unmerge combined.fastq out_template
+    Usage: fastqutils unmerge {options} combined.fastq out_template
 
     Options:
       -gz    gzip compress the output files