Bedtools -Sorted Genome File
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.
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finswimmer
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gtasource
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gtasource
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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
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