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Old 09-12-2012, 10:01 AM   #2
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Location: Cambridge, UK

Join Date: May 2010
Posts: 311

Originally Posted by shyam_la View Post
Lets say I have an excel file, one column with chr number and the next with genomic coordinates, running into several thousands in numbers. Is there some online / offline tool into which I can input this information and get as output the nucleotides at these loci in hg19?

For eg.
1 23354
2 345344
3 43543553

1 23354 T
2 345344 C
3 43543553 A
If could reformat your excel file to BED format (even within excel) and save it as plain text (say as mypositions.bed). Then, you can use bedtools as something like (assuming you have already the FASTA file for hg19):

bedtools getfasta -fi hg19.fa -bed mypositions.bed -tab
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