Ensembl bacterial genome alignment - use top level or chromosome?

Question

[Boboboe]

Hi all,

I'm trying to align my sequecing data to a whole genus of bacteria. There are multiple files for each bacteria - there are chromosome, top level, and non-chromosomal.(an example of what I'm looking at:ftp://ftp.ensemblgenomes.org/pub/bacteria/release-40/fasta/bacteria_0_collection/mycobacterium_tuberculosis_h37rv/dna/) While most bacteria has top level available, not all have chromosome available. From what i understand, top level basically contain all the stuffs that are assembled into a chromosome and even those that are not.(more info in this readme: ftp://ftp.ensemblgenomes.org/pub/bacteria/release-40/fasta/bacteria_0_collection/mycobacterium_tuberculosis_h37rv/dna/README) I was just wondering if I should use top level or chromosome for reference to align my reads to. Thanks!

Answer 1

[Emily]

Yes, your interpretation is correct. Top-level will also contain some unplaced scaffolds (possibly from plasmids) so if you want to align your reads to those, you should include them.