question about homer

Question

[13719756608]

hello,everyone i was looking for motif for my m5c-seq bed file,and i encounter some problem this is my bed file: MACS_peak_18032 Chr22 2938644 2938798 . MACS_peak_18038 Chr22 3187304 3187410 . MACS_peak_18039 Chr22 3203939 3204154 . MACS_peak_18040 Chr22 3238473 3238508 .

this is my code:

findMotifsGenome.pl m5C-control-1.mRNA.m5C.motif.bed danRer11 ./m5c-control-1.mRNA.m5C.motif.output/ -size 200

danRer11 is the zebrafish genome,and the homer response was:

!!! Something is wrong... are you sure you chose the right length for motif finding? !!! i.e. also check your sequence file!!!

can someone help me figure out what was wrong and how i can solve this problem,thank u

[boczniak767]

I suppose there is problem with your bed file, the first column should be chromosome name, take a look at bed file specification. From your bed it seems you have "MACS_peak_1803" in the first column.