Update quantifier.pl

README.md

@@ -439,15 +439,37 @@ mature/star sequence is determined.
 
 #### Options
 
-| option | description                                                        |
-|--------|--------------------------------------------------------------------|
-| `‑t`   | list all values allowed for the species parameter that have an entry at UCSC |
+| option       | description                                                                                  |
+|--------------|----------------------------------------------------------------------------------------------|
+| -p [file.fa] | miRNA precursor sequences (around 70bp: One line per precursors sequence)
+| -m [file.fa] | mature miRNA sequences (around 22nt)
+| -P           | specify this option of your mature miRNA file contains 5p and 3p ids only
+|	-c [file]    | config.txt file with different sample ids... or just the one sample id  -- deprecated
+|	-s [star.fa] | optional star sequences from miRBase
+|	-t [species] | e.g. Mouse or mmu
+|	             | if not searching in a specific species all species in your files will be analyzed
+|	             | else only the species in your dataset is considered
+|	-y [time]    | optional otherwise its generating a new one
+|	-d           | if parameter given pdfs will not be generated, otherwise pdfs will be generated
+|	-o           | if parameter is given reads were not sorted by sample in pdf file, default is sorting
+|	-k           | also considers precursor-mature mappings that have different ids, eg let7c
+|	             | would be allowed to map to pre-let7a
+|	-n           | do not do file conversion again
+|	-x           | do not do mapping against precursor again
+|	-g [int]     | number of allowed mismatches when mapping reads to precursors, default 1
+|	-e [int]     | number of nucleotides upstream of the mature sequence to consider, default 2
+|	-f [int]     | number of nucleotides downstream of the mature sequence to consider, default 5
+|	-j           | do not create an output.mrd file and pdfs if specified
+|	-W           | read counts are weighed by their number of mappings. e.g. A read maps twice so each position 
+|              | gets 0.5 added to its read profile
+|	-U           | use only unique read mappings; Caveat: Some miRNAs have multiple precursors. These will be 
+|              | underestimated in their expression since the multimappers are excluded
+| -u	         | list all values allowed for the species parameter that have an entry at UCSC
 
 #### Example usage
 
 ```sh
-quantifier.pl precursors.fa mature.fa reads.fa star.fa/none species/none \
-  timestamp/none pdf
+quantifier.pl -p precursors.fa -m mature.fa -r reads.fa
 ```
 
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