Bedops for extracting fasta sequences from bed file

[chudar]

Hi,

I am new to bedops and I have bed file like following

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bed_file
scaffold123    56    120    transcript_A
scaffold123    175  234    transcript_A
I would like to extract the fasta sequence from the from the respective scaffold in genome.fasta with transcript header. Using bedtools this can be acheived by

Code: [Select]

bedtools getfasta -name fi genome.fasta -bed bed_file Is it possible to achieve the same output using bedops. Kindly guide me.

[AlexReynolds]

BEDOPS works with BED files and leaves work on FASTA files to other toolkits.

If you're looking for an alternative to bedtools, you might investigate samtools faidx.

Some examples here:

• https://www.biostars.org/p/183629/#183633
• https://www.biostars.org/p/98725/#98733