Gff3 files for H.pylori strains

[Caroline Plus]

Hello,

We are doing differential analysis (DE) in DeSeq for different H.pylori strains. We are not able to find the gff3 files for those H.pylori strains (98-10, 35A, 51, 52, F16, F30, F32, F57) to use in htseq-count.

Perhaps you will know where I can download those gff3 files? The fasta files can be downloaded from NCBI, but not the gff3 ones.

Thanks

[cliffbeall]

They are in NCBI, at least where I get bacterial genomes (which changed recently).

In the subfolders of this directory: NCBI Helicobacter genomes the files that end in .gff.gz are gzip compressed gff3 files, here is the top of one:

##gff-version 3
#!gff-spec-version 1.21
#!processor NCBI annotwriter
#!genome-build ASM852v1
#!genome-build-accession NCBI_Assembly:GCF_000008525.1
##sequence-region NC_000915.1 1 1667867
##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=85962

[piet]

Perhaps you will know where I can download those gff3 files?

http://togows.dbcls.jp/entry/nucleotide/CP002605.1.gff

[cliffbeall]

Sorry, I missed that you had a specific list of strains - I think you can find the genome accessions in this table so you know which folders to look at:

http://www.ncbi.nlm.nih.gov/genome/genomes/169