all the peaks of MACS2 BED file starting at position 0

Question

[salamandra]

At least 2 peak files (.BED) given by MACS2 have all the peaks of the file starting at position 0 even in different chromosomes.

This is an odd coincidence. Does any of you known of any reason (bad formatted input file or other) that could explain this?

The input SAM files have different starting positions.

Bellow is the script:

#!/bin/bash
TRT=/path/ChIP_FOS_CD49f.SAM
CTRL=/path/Input_FOS_CD49f.SAM
NAME=macs_chipvsinput_FOS_day2
macs2 -t $TRT\ 
-c $CTRL \ 
-g hs \
-n $NAME \
-f SAM \ 
-B \
-p 24

[poisonAlien]

why is your p-value cut-off set at 24 ? macs2 command, shouldn't it be macs2 callpeak ? Is there any particular reason your alignment files are in SAM format ? (BAM is better, compressed and binary so it won't get messed up, unlike SAM which is just a text file)

[salamandra]

thanks i'm trying your suggestions to see if works. i though -p was the number of CPUs..my bad