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Hi I am working with CHIP-Seq Single end data. I have performed peak detection using the MACS14 . Now I need to convert thus obtained bed file to fasta format. I tried bedtools although it was not useful. Please let me know how i can convert the bed file to fasta so that I can perform motif detection on this data using MEME.
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THANKS for your prompt response!!!
Yes, I worked with fastafrombed option but it gave me errors while doing this, I have searched in google regarding the error but no use.
Do I need to provide the genome file for converting the bed to fasta. Also please tell me the format of the genome file and steps to do it.
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MEME motif discovery
I have performed the motif detection using MEME, it resulted me with the motif of 50 bp now and later I have performed the motif search using the TOM TOM and I have got some three known motifs with 30 bp each. Now i am confused with the obtained motifs, is it common to get motifs with 50 bps? Any suggestions will be appreciated
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