I have a seemingly simple task to calculate aggregate profiles from paired-end ChIP-seq data. But I have problems with HOMER with respect to this. I have SAM files with paired-end mapped reads, as well as BED files oftained from those SAM files. The information about read pairs is lost in the BED obviously.
Using HOMER with BED files without the knowledge of read pairs resulted in reasonably good profiles. HOMER estimated that the average fragment lengt is 214 bp.
Then I wanted to improve the profiles and recalculated everything (starting from HOMER tag directories) based on the initial SAM files using -sspe option. The resulting profiles are much smoother but all interesting fine details seen previously are lost, and also I am confused that now HOMER reports the average fragment length 105 bp.
Thus, it seems that -sspe option in HOMER works wrongly.
P.S. Then I tried creating tag directories from paired-end SAM without -sspe option (against what is written in the HOMER user manual) and it seems that HOMER works fine.
Anyone encountered problems like this with HOMER? Any suggestions?