Hi everyone,
Is there people interested in ChIP-seq analysis ?
I did not see too much threads on this topic...
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 as describe on solidsoftwaretools.com 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.
Is there people interested in ChIP-seq analysis ?
I did not see too much threads on this topic...
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 as describe on solidsoftwaretools.com 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.