My goal is to retrieve the promoter regions of a few hundred genes. I have the primary transcripts of these genes in a FASTA file and the organism's genome in another FASTA file.
How can I align the transcripts to the reference genome and then retrieve 200nt of genomic sequence upstream of the transcript?
Thanks for the help!
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written
by
mmaselko •
2 answers
You could use Blat to align the transcripts to the genome, once you have the coordinates, you could create a bed file of 200 nt upstream of the alignment start and use getFasta of BedTools suite to retrieve the promoter sequence from the reference genome.
http://bedtools.readthedocs.org/en/latest/content/tools/getfasta.html
In addition, you can also use GMAP to align the transcripts to genome. Check this tutorial for more information.
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written
by
Prakki Rama
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