Bedtools -Sorted Genome File

Question

[gtasource]

Bedtools coverage says to use the -sorted option for bedtools coverage, I need to provide a genome file that:

Defines the expected chromosome order in the input files for use with the -sorted option.

How is the file supposed to look? I included one that listed out all of the chromosomes, but received an error that genome file has no valid entries.

Answer 1

[finswimmer]

Hello gtasource,

this file needs the chromosome name and the length of the chromosomes. You can extract these information from your alignment file as the information are in the header:

$ samtools view -H file.bam|grep @SQ|sed 's/@SQ\tSN:\|LN://g'' > genome.txt

fin swimmer