How to extract genomic sequence using genomic coordinates
These are the set of sequence a very small subset
chr1_6237786_6251176_F
chr1_10150615_10150781_R
chr1_12911118_12934193_R
chr1_13142230_13142459_R
chr1_13640475_13640801_R
chr1_13640480_13640801_R
I want to extract the set of sequences that lies with my coordinates as i have put above ..how to do that, do i use an lets say hg38 chromosome to parse the coordinates ,any help or suggestion would be highly appreciated ..
2 answers
Hi, you convert to BED format and use "getfasta" from bedtools. For details, "http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html".
Example for BED file of your sample
chr1 6237786 6251176 x y +
chr1 10150615 10150781 x y -
chr1 12911118 12934193 x y -
chr1 13142230 13142459 x y -
chr1 13640475 13640801 x y -
chr1 13640480 13640801 x y -
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Puli Chandramouli Reddy
No..
you need to convert your co-ordinates to BED file format. I assumed that your sample file is co-ordinate file.
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Puli Chandramouli Reddy
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this question was asked many times here, search the site please: e.g: Extract User Defined Region From An Fasta File
thank you i will look into it