This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How To Fetch Sequence From Chromosome Coordinates

Hi all

I have chromosome coordinates (e.g. 5233922 to 5235189 of chr18). how can I get the sequence corresponding to this region ? Like this I have huge file containing chr1 to chr21 and chr X and chrY. Is there any platform where I can give the coordinate file and that give me the desired nucleotide sequences ?

Is there any difference between using hg18 human reference genome or hg19 for the same purpose. Because the experiment has used hg18 assembly to generate the coordinates (which they have given in supplementary material).

Thanks in advance. KD

chromosome coordinates
• 16,193 views • link
updated by Istvan Albert Istvan Albert • written by monukmr98 monukmr98

A suggestion to closing posts - if it is a duplicate could we rather put this into the answer and close it that way. Because the question is technically answered only that the answer is in another location. This helps later when we run statistics on how many questions are open/unanswered etc. I would consider a duplicated question as being answered.

Now I am considering adding a new command called \dup that will both close and answer the question all in one shot.

• 0 views • link
written by Istvan Albert Istvan Albert

1 answer

As Pierre said it is a duplicate of

How to get the sequence of a genomic region from UCSC?

and

Extract sequence from the genome?

• 0 views • link
written by Istvan Albert Istvan Albert

Log in to answer this question.

More posts like this