NC_000913.2 to the Genomes server

[Peter Brazda]

Hi, 

  Could you add the Escherichia coli MG1655, NC_000913.2 ref seq to the Genomes server? I failed to create a genome from the fasta file. I guess because I could not get the right genefile (gff) for it.

Thank you!

(If you could include a step-bt-step protocol for creating a new genome after having the fasta file, that could also help. I have already checked the IGV website/help, etc.)

FASTA link:

http://www.ncbi.nlm.nih.gov/nuccore/NC_000913.2?report=fasta&log$=seqview

Best, 

Peter

[Peter Brazda]

I have found this post:

https://groups.google.com/forum/#!topic/igv-help/MSMJrdHPdG8

 So my real problem is not creating a reference genome, but having one with the genes, features in it.

Thanks for any help!

Best, 

P

[Jim Robinson]

Hi,

The step-by-step guide is here:  http://www.broadinstitute.org/software/igv/LoadGenome

Having said that, we already host that genome.   Did you have trouble finding or loading it?   See the screenshot below

[Emily Tai]

Hi Jim,

NCBI has a newer version of E.coli genome,NC_000913.3, which has two insertions, 1.9kb longer and is the substrain we are working on.  I downloaded the latest fasta and gff files from <http://www.ncbi.nlm.nih.gov/genome/?term=E.coli> and tried to create .genome file following the instruction on <https://www.broadinstitute.org/software/igv/LoadGenome>.  However, I got an error message "Unexpected error while importing a genome: An error occurred while accessing: /Users/taic/project/Ecoli/reference/Ecoli_K12_MG1655.gff

Fasta file has uneven line lengths in config null".  The log files is attached.  Any suggestion how to fix the problem?     

Or does Broad Institute plans to host the genome NC_000913.3 in the near future?

Thanks for your feedback!

Cheers,

Emily,

[Emily Tai]

Hi Jim,

I was able to create the NC_000913.3.genome file now.  Thanks anyway.

Emily,

[Jim Robinson]

Great, if you don't mind me asking how did you do it?   I got stuck on breaking up the enormous gtf file.

Jim

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/1f038e26-113d-42d5-879a-46de948b55c2%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.