How to extract Ensemble GeneBank Annotation file

[HTnoob]

I have downloaded 1.3 gb from here:

http://www.ensembl.org/info/data/ftp/index.html

Called "Annotated sequence (GenBank)" for Homo Sapiens.

This is quite a few *.dat.gz files, but how do I get the .gbk (gene bank) file extracted?

[HTnoob]

What Im looking for is a "GRCh37.74.gbk" file with annotations.

Or I would actually prefer the NCBI hg19 version.

[GenoMax]

Genbank format files for each chromosome are available here: ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/

Ensembl 37.74 annotation file: ftp://ftp.ensembl.org/pub/release-74...Ch37.74.gtf.gz

NCBI annotations: ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/GFF/

[HTnoob]

Thank you very much!
These look interesting, thought Im not sure whats the difference..

ref_GRCh37.p13_scaffolds.gff3.gz
ref_GRCh37.p13_top_level.gff3.gz


Also, how may I convert from gff3 –genbank?

[GenoMax]

Thank you very much!
These look interesting, thought Im not sure whats the difference..

ref_GRCh37.p13_scaffolds.gff3.gz
ref_GRCh37.p13_top_level.gff3.gz


Also, how may I convert from gff3 –genbank?

Explanations are in this README file: ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/README

{alt,ref}_{assembly_name}_scaffolds.gff3.gz
-------------------------------------------
Features annotated on {assembly_name} in scaffold coordinates.

{alt,ref}_{assembly_name}_top_level.gff3.gz
-------------------------------------------
Features annotated on {assembly_name} in top-level object coordinates.
The top-level objects are: assembled chromosomes, unlocalized
scaffolds (those scaffolds that are associated with a specific
chromosome but which cannot be ordered or oriented on that
chromosome), unplaced scaffolds (those scaffolds that are not
associated with any chromosome), and in some cases scaffolds from
alternate locus groups or genome patches (see the NCBI Assembly Model
web page for an explanation of these terms:
http://www.ncbi.nlm.nih.gov/genome/assembly/model).

If you can explain what is it that you are trying to do then there may be a simple option available.

[HTnoob]

Thank you again!

Im trying to set up a searchable SNPs database, as described here:

http://www.biomedcentral.com/1471-2105/14/326

To make the database I need two files, my reference genome used to make the VCF file (in EMBLE or GENBANK) along with the actual VCF file. Like this:

snp-search -create -d my_snp_db.sqlite3 -r my_ref.gbk -v my_vcf_file.vcf


I used the NCBI hg19 genes.GTF annotation file. Best thing would be to convert this to GTF to Genbank/EMBLE. But I had no luck in doing that..

[GenoMax]

I do not think there is a single genbank file available for human genome. There are genbank files available for individual chromosomes. I suppose you could merge them into a single file.

The paper you referred to above seems to be using small files (plasmids) for creating the database. You will need to check if that can handle a human genome size dataset.

On a different note why aren't you searching against dbSNP and what do you want to get from the search (sequence?)

[HTnoob]

Good points!

We have ran GATK on RNAseq samples and want to explore the results, personally I don't know which questions might be answered?

[Stroehli]

Hi HTnoob,
I ran into the same problem trying to run snp-search. I will try to find a solution for this issue. Meanwhile, if you come up with a good solution I would appreciate you posting it here.

Cheers