Question: Unable to find this E coli genome
0
gravatar for pomodoro_sinensis
6 weeks ago by
pomodoro_sinensis0 wrote:

Hello,

I am trying to download the E. coli genome used by the following paper (https://science.sciencemag.org/content/early/2020/12/16/science.aba5257)

It says as follows:

...where the cDNA reads were mapped to either a combined B. subtilis – E. coli genome [ASM904v1.45 and ASM80076v1.37 from EnsemblBacteria (57)] or only...

I can find the B. subtilis genome without any problem. But I am unable to find the E. coli one. Might this be a typo?

Thanks!

ADD COMMENTlink modified 6 weeks ago by Mensur Dlakic9.0k • written 6 weeks ago by pomodoro_sinensis0
0
gravatar for Mensur Dlakic
6 weeks ago by
Mensur Dlakic9.0k
USA
Mensur Dlakic9.0k wrote:

Here is the description:

https://www.ncbi.nlm.nih.gov/assembly/GCF_000800765.1/

Full directory:

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/800/765/GCA_000800765.1_ASM80076v1/

Genomic DNA:

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/800/765/GCA_000800765.1_ASM80076v1/GCA_000800765.1_ASM80076v1_genomic.fna.gz

ADD COMMENTlink written 6 weeks ago by Mensur Dlakic9.0k

Wow thank you!! Do you happen to know why there is no transcriptome in the full directory? (i.e. a cdna.all.fa file) Or is it me who is not finding it?

ADD REPLYlink written 6 weeks ago by pomodoro_sinensis0

Also, where did you click here: https://www.ncbi.nlm.nih.gov/assembly/GCF_000800765.1/

to get to the full directory?

ADD REPLYlink written 6 weeks ago by pomodoro_sinensis0

cDNA file:

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/800/765/GCA_000800765.1_ASM80076v1/GCA_000800765.1_ASM80076v1_cds_from_genomic.fna.gz

Click on FTP directory for GenBank assembly

ADD REPLYlink written 6 weeks ago by Mensur Dlakic9.0k

Thanks so much!! I know there are no introns in bacteria, but still cDNA is not the collection of CDSs, am I right? A 5' or 3'UTR is part of the cDNA but not of the CDS. Is it called CDS because it doesn't include those sequences? Or is it just the way of calling the cDNA (UTRs and CDS) in bacteria's files?

ADD REPLYlink written 6 weeks ago by pomodoro_sinensis0

Here is an example of a B subtilis file for cDNA (corresponding to the other genome that appears in my initial message).

ftp://ftp.ensemblgenomes.org/pub/bacteria/release-49/fasta/bacteria_0_collection/bacillus_subtilis_subsp_subtilis_str_168_gca_000009045/cdna/Bacillus_subtilis_subsp_subtilis_str_168_gca_000009045.ASM904v1.cdna.all.fa.gz

Do you happen to know if this file different from the one you sent, or is it a matter of nomenclature?

ADD REPLYlink written 6 weeks ago by pomodoro_sinensis0
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