Hello there,
I am following the cisgenome online tutorial for 2-sample chip-seq analysis. I compare the median of peak length calculated from hts_peakdetectorv2_2sample -br 0 -ssf 0 and -br 1 -brl 30 -ssh 1.
The difference of median is very large: 199 and 88 bp. Is it normal? Can boundary refinement and single strand filtering affect the peak length so dramatically?
Another question following up is should we just use default value with no br and ssf or should we use the parms in the tutorial?
Thanks.
I am following the cisgenome online tutorial for 2-sample chip-seq analysis. I compare the median of peak length calculated from hts_peakdetectorv2_2sample -br 0 -ssf 0 and -br 1 -brl 30 -ssh 1.
The difference of median is very large: 199 and 88 bp. Is it normal? Can boundary refinement and single strand filtering affect the peak length so dramatically?
Another question following up is should we just use default value with no br and ssf or should we use the parms in the tutorial?
Thanks.
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