Fragment length

[Shmuel]

Hi,

1) I want to see how peaks from macs2 (converted to BAM via bedtobam) are located relative to the TSS. What should be the fragment length parameter in such a case?  

2) Theoretical question: In case that the supplied fragment length (-FL parameter) is shorter than the length of the peaks, will the peaks (passed as reads to ngsplot) be shortened to that fragment length?