Hello Seq_Community!!

[Ayyappa_kumar]

Hello Seq_Community!! I work in INDIA, developing my understanding about sequence data analysis and am here to learn and exchange support!

[Ayyappa_kumar]

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.

[GenoMax]

Did you try fastafrombed and did that not work?

Are you trying to do this without downloading a local copy of the genome?

[Ayyappa_kumar]

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.

[GenoMax]

Genome file needs to be in fasta format (multi fasta if there are more then one chromosome).

$ fastaFromBed -fi genome.fa -bed your_bed_file.bed -fo data_extracted.fasta

[Ayyappa_kumar]

Can I concatenate all the chr.fa files using cat option, and can create the genome. Later will I be able to use the above utility.

[GenoMax]

Yes that should work .. as long as you are using the same genome build/files that you used for the original alignments and the chromosome names match what is in your bed file.

[Ayyappa_kumar]

It works !!!!

Thanks for your help.

[Ayyappa_kumar]

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