Update README.md

README.md

@@ -1,15 +1,15 @@
 # compareBed.sh for filtering of new, yet unannotated motifs 
 
 The script mainly utilizes bedtools for comparison.
-The sequences in the bed-file from the experiment are compared to a bed-file of sequences of known motifs.
+The sequences in the bed-file of the experiment are compared with sequences of known motifs, also in bed-format.
 Only sequences with no overlap with the known-motif sequences are selected in the first step.
 Then the overlapping parts of overlapping sequences are also selected as new sequences.
-The resulting bed-file contains the sequences selected in the two steps. The file has two extra columns appended: 1st the DNA sequence of the entry and 2nd a flag with possible values '1' or '0' for 'no_overlap' or 'overlap' of the maximum score region of the entity with any known-motif sequence.  
+The resulting bed-file contains the sequences selected in both steps. The output file has two extra columns appended: 1st, the DNA sequence of the entry, and 2nd, a flag with possible values of '1' or '0' for 'no_overlap' or 'overlap' of the maximum score region of the entity with any known-motif sequence.  
 
-Apart from the experiment data (bed-format) of sequences with possible motifs, another bed-file of the sequences with known motifs and a genome file in fasta format are required.
+Apart from the experiment data (bed-format) of sequences with possible motifs, another bed-file of the sequences with known motifs and a genome file in fasta format are required. The bed-file with known motif sequences can be calculated with the tool motifscan.py.
 
 For usage, run ./compareBed.sh 
 
 dependencies:
-- R
-- 
+- R ?version
+- bedtools ?version