http://solidsoftwaretools.com/gf/ Gforge Advanced Server RSS kevin lebrigand <lebrigand@ipmc.cnrs.fr> Hi everyone, Well, I need to analyse ChIP-seq data from solid v3 system. I've used Sissrs and Macs for the peak detection but it seems that i do not find the same peaks in each analysis... Maybe this is due to the parameters i've used, but i look only for the moment for the 50 best peaks in term of Fold enrichment and i thought that it could be more or less the same peaks. Well i'm a bit disappointing, any help could be very appreciated. Here is the command lines i've ran for peak detection : Sissrs : perl sissrs.pl -i xxx.bed -o sissrs.bed -s 3080000000 -F 50  -L 100 -w 50 -b control.bed Macs : python macs -t xxx.bed --tsize=50 --format=BED --nomodel --name xxx --bw=100 --control=control.bed Anyway, i've developped a script running the SOLiDTM 3 System Application for ChIP Sequencing Analysis and i want to test it with the dataset from the nature method paper on FOXA3 IP on solid (Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD™ system). If someone know how to get the dataset i did not find it on the web. Thanks for any help, kevin.