Originally posted by jalapea
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In what format is the information about the genes (coordinates) you want to extract? -
extract the genes
I'm trying to extract the genes of a chromosome that is in fasta file, you can help me on how to do a script, thanksLeave a comment:
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Try the program fastaFromBed in bedtools:
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Extracting sub-sequences from a larger DNA sequence using a file of coordinates
Hi,
I am looking to extract and annotate the sequences of a large number of genes from a series of very large (whole chromosome) consensus sequences.
I have a file identifying the gene names and physical locations (.bed file) on their respective chromosome. There are too many genes to manually locate each one, so I need to find a way to automate this process.
Does anyone know of a script or program that can extract DNA sub-sequences using a series of coordinates?
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