Ensembl bacterial genome alignment - use top level or chromosome? · Biostar

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Ensembl bacterial genome alignment - use top level or chromosome?

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!

chip-seq alignment ensembl bacteria chromosome

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updated 7.8 years ago by Emily

• written 7.8 years ago by Boboboe •

1 answer

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.

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written 7.8 years ago by Emily

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