coverageBed -abam

[mmmm]

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

[larsgt]

Could you have a problem similar to this?

https://code.google.com/p/bedtools/issues/detail?id=103

[mmmm]

any other suggestions please for this issue

[larsgt]

If you include the a short example of the two files it might enable a better chance of identifying the problem. I don't know if coverageBam only wants bed files or if it's ok with gff. Also check that the line breaks in the file are correct for your platform or make a small test example you know should work.

[mmmm]

gff annotation file

in general, where do we get gff file from?, or woulf it be better to annotate the reference genome using RAST for example