Question: How do I perform a motif search on a specific fasta sequence?
0
gravatar for a.rex
15 months ago by
a.rex190
a.rex190 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 • 935 views
ADD COMMENTlink modified 15 months ago by RamRS25k • written 15 months ago by a.rex190
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 15 months ago by steve2.4k

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

ADD REPLYlink written 15 months ago by lieven.sterck6.4k
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