Hi:
I have used PureClip to analyze the an eClip-seq dataset and get the bedfile. Now I want to get the binding motif of the RBP, so I installed MEME to call motif from the bedfile.
The head of my bed file is like this:
head file.bed
chr1 633991 633992 3 14.891 + [score_CL=14.891;score_E=55.5259;score_B=56.5133;score_UC=14.891] chr1 633992 633993 3 13.9207 + [score_CL=13.9207;score_E=55.7616;score_B=56.7817;score_UC=13.9207] chr1 633993 633994 3 8.62409 + [score_CL=8.62409;score_E=55.9413;score_B=44.2988;score_UC=8.62409] chr1 633997 633998 3 2.33843 + [score_CL=2.33843;score_E=52.7415;score_B=28.4546;score_UC=2.33843] chr1 633998 633999 3 5.65288 + [score_CL=5.65288;score_E=50.1933;score_B=32.0494;score_UC=5.65288] chr1 633999 634000 3 5.54813 + [score_CL=5.54813;score_E=48.5419;score_B=31.9227;score_UC=5.54813] chr1 634009 634010 3 0.880815 + [score_CL=0.880815;score_E=44.1986;score_B=22.3018;score_UC=0.880815] chr1 634010 634011 3 0.782717 + [score_CL=0.782717;score_E=45.8173;score_B=22.1729;score_UC=0.782717] chr1 1037335 1037336 3 0.189687 + [score_CL=0.189687;score_E=57.7691;score_B=25.1448;score_UC=0.189687] chr1 1037336 1037337 3 0.277321 + [score_CL=0.277321;score_E=55.6412;score_B=25.2031;score_UC=0.277321]
So I get fasta file from the bed file using bedtools:
bedtools getfasta -fi GRCh38.primary_assembly.genome.fa -bed file.bed -s -fo file.fasta
and run MEME like this:
meme file.fasta -mod anr -o RBP_MEME_anr_motif6 -rna -nmotifs 6 >log015 2>error015
But I get nothing except the following feedback:
Writing results to output directory 'PureCLIP_HNRNPK_MEME_anr_motif6'. BACKGROUND: using background model of order 0 PRIMARY (classic): n 13474 p0 13474 p1 0 p2 0 SEQUENCE GROUP USAGE-- Starts/EM: p0; Trim: p0; pvalue: p0; nsites: p0,p1,p2 All sequences must be at least 8 characters long. Set '-w' or '-minw' or remove shorter sequences and rerun.
From the bedfile I see the sequence is about 3bp long, how should I fill the condition of at least 8 characters long?
Can anyone help me on this? Thank you very much.