<p>how do I convert fa files to bed format?</p>

<p>This is a good, though slightly misguided question. If you want to make a BED file from a FASTA sequence, you might do something like this:</p>
<ol>
<li>Find your FASTA sequence. We'll use <a href="http://goo.gl/DsnN5">human hemoglobin beta</a> as an example. </li>
<li>Use BLAST to <a href="http://goo.gl/fEMO5">align your sequence</a> to the human reference genome.</li>
<li>In the alignment example above, you would pick the genomic alignment, not transcript, and choose "subject" start and end positions. Note that this example has 3 exons, so your BED file start would be 5186957 and end would be 5188159.</li>
<li><a href="http://goo.gl/HVfOc4.">Create a BED file</a> using the chromosome (11 in above example), chromstart (5186957), chromend (5188159), and a name for your gene (HBB). You can then upload this as a custom track in the UCSC genome browser.</li>
<li>You will probably want to add introns to your gene structure, so at this point you can the <a href="http://goo.gl/whi4t">GenePred format</a> instead of BED. This allows you to specify the strand, as well as introns, exons, and transcription factor binding sites.</li>
</ol>