Filter Genome for Specific Sites
Hello,
I have a list of ~1,300 single bp sites and a fully annotated genome. I'd like to create a fasta file with only the 1,300 sites (with ±300 bp on each side). My sites are in an Excel file right now with chromosome, position, strand, correlation, p-value as 5 separate columns. Does anyone know of a program/function that will subset a genome into the 1,300 sites/regions?
Thank you in advance!
1 answer
I have a list of ~1,300 single bp sites
Convert your file to plain text BED format (three fields required).
Use bedtools slop to extend the range by 300 bp --> Extend The Coordinates Entries Within A Bed File
Then use bedtools getfasta or samtools faidx to extract the sequence.
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This is unhelpful and doesn't answer my question.