need your advice please-
when I am using bedtools to locate missing genes from my assembled strain compared to the reference genome, I got (0) values for all genes although I am very sure that my strain is very similar to the reference strain- I am not sure what could be wrong
coverageBed -abam input.sorted.bam -b reference.gff3.txt > output.coverage.txt
(I obtained the gff file from ftp.ncbi.nih.gov/ genomes and saved it as tad delimited
when I am using bedtools to locate missing genes from my assembled strain compared to the reference genome, I got (0) values for all genes although I am very sure that my strain is very similar to the reference strain- I am not sure what could be wrong
coverageBed -abam input.sorted.bam -b reference.gff3.txt > output.coverage.txt
(I obtained the gff file from ftp.ncbi.nih.gov/ genomes and saved it as tad delimited
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