Update Readme (FilterLow script readme)

README.md

@@ -1,4 +1,34 @@
 ReannTE
 =======
+Last Update: 2014 08 06
+
 
 Scripts to help transposable elements consensus sequences curation
+
+
+
+========================================================
+ReannTE_FilterLow.pl
+
+     WHAT IT DOES: 
+	 This script uses Repeat Masker to mask low complexity / simple repeats of the input fasta file
+	 (for example, RepeatScout output)
+	 
+	 It eliminates the ones that are more than XX% masked (-p option)
+	 2 fasta outputs: retained sequences and rejected sequences
+	 	 
+	 perl <scriptname.pl> -i <fa> [-r <RMpath>] [-p <XX>
+
+     MANDATORY ARGUMENTS:
+	 -i <fa>    => fasta file
+
+     [OPTIONAL ARGUMENTS]:
+	 -r <path>  => path = localisation of repeat masker software
+	                  if no path provided, path = /home/software/RepeatMasker		          
+	 -p <XX>    => XX = threshold, in % (default = 80%). It sets the minimum low complexity masked % required to eliminate the sequence
+	                  
+     REQUIREMENTS:
+	 - Repeat Masker software, crossmatch engine
+	 - Bioperl (Bio::DB::Fasta, Bio::SeqIO)
+
+