How to extract ~2M short sequences based on coordinates from a 3G fasta file?
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15 months ago
kynnjo ▴ 40

(Sorry for the Bioinformatics 101 question!)

I have a file with ~2 million sets of coordinates (chromosome<tab>begin-position<tab>end-position), corresponding to short (~50nt) human genomic sequences (hg19). I want to extract the actual sequences from a human genome assembly 19 fasta file (~3.0G).

I imagine this is a relatively common task, and therefore, that there must be standard tools to carry it out efficiently.

Sadly, my Google fu has not been up to the task of finding them.

I would appreciate not only the name of a tool to use, but also the command line one would use, especially if there are important flags and options I should be aware of when using such a tool.

genome assembly sequence • 270 views
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Entering edit mode
15 months ago
kynnjo ▴ 40

Shortly after I posted this question I found that samtools faidx -r <regions_file> ... does what I need.

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