Understanding the output

[pna059]

Hi,
I use the SmartMap for my plant genome ChIP-seq data (60% multimappers using standard bowtie2 mapping.)
After SeqMapPrep and SeqMap (default with -r and -c), I got the list of these files:
sample_reads_uniterated.bed.gz
sample.log
sample_iteration-1_reads_iterated.bed.gz
sample_iteration-1.bedgraph.gz
sample_iteration-0_reads_iterated.bed.gz
sample_iteration-0.bedgraph.gz
splits
sample_vf_k51_I100_X250_filt-flag_filt-coord_scores.bed.gz

To make sure that I understand the output correctly: the 'sample_vf_k51_I100_X250_filt-flag_filt-coord_scores.bed.gz' contains both the uni and 51 locations of all multimappers which is then processed into the iterated bed files. Should I automatically use the 'sample_iteration-1_reads_iterated.bed.gz' file (containing uni + the best mutimapping locations?) to do the peak calling and generate normalised coverages?

Thank you,

Pavla