Question: How do I perform a motif search on a specific fasta sequence?
0
gravatar for a.rex
6 months ago by
a.rex180
a.rex180 wrote:

I have an annotated genome file, and I have a potential ncRNA that could be an eRNA.

I have extracted this sequence to a fasta file, and want to use homer for scanning transcription factor binding sites (i.e. to work out whether it is a potential enhancer).

How can I do this? I have tried with this command but it comes up with the error:

 perl findMotifs.pl input.fa fasta motifResults/ -fasta genome.fa 

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

Scanning input files... !!! Something is wrong... are you sure you
chose the right length for motif finding? !!! i.e. also check your
sequence file!!!
enhancer homer • 413 views
ADD COMMENTlink modified 6 months ago by RamRS20k • written 6 months ago by a.rex180
1

If you already have the fasta file then I would just use MEME-ChIP; http://meme-suite.org/tools/meme-chip

ADD REPLYlink written 6 months ago by steve1.9k

Can you post an extract of the fasta file(s) you're using?

ADD REPLYlink written 6 months ago by lieven.sterck4.2k
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