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

<p>You can't.</p>
<p>A <strong>Fa/Fasta</strong> file describes a sequence of DNA/Protein:</p>
<pre><code>&gt;Name
ATAGCTACGATTACGACGTACG
ATCGATCGATGCATCAGCTACT
AACTAGTCGATGATGCATACG...
</code></pre>
<p>A <strong>bed</strong> file describes some features mapped on a genome/sequence:</p>
<pre><code>chr1  786 9879 gene1
chr2  486 979  gene2
</code></pre>
<p>The only thing you can do is saying that the BED contains only one feature: your sequence:</p>
<pre><code>Name  0  1098 Name
</code></pre>