Question: I want to convert a fasta file to a bed file Edit
Answer: Here's what you need to do.
1) Find your FASTA sequence. We'll use human hemoglobin beta as an example.
2) Use BLAST to align your sequence to the human reference genome.
3) 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.
4) Create a BED file 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.
5) You will probably want to add introns to your gene structure, so at this point you can the GenePred format instead of BED. This allows you to specify the strand, as well as introns, exons, and transcription factor binding sites.
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