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No E coli BW25113 genome?

asked 2017-06-12 07:10:40 -0600

Arya Gupta gravatar image


I want to analyse HiSeq data of some E coli mutants. I have the BAM files for the mutants, but as there is no reference (or none that I can see), I am unable to generate a plot.

I have tried to convert the fna.gz available for BW25113 to .tsf to try and use it as a reference with no luck. Is there a way round this?

Many thanks, Arya

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answered 2017-08-09 11:47:57 -0600

SteveHystad gravatar image

Hi Arya,

Unfortunately we do not currently support the E.coli BW25113 genome assembly. Typically, an allele reference sequence source can be built for any species where there is an available DNA sequence (FASTA) file. The Convert Wizard that is available within the software can directly support conversion of the GTF formatted data. The Convert Wizard can be accessed by going to File > Add then clicking Convert in the lower left corner of the Data Source Library. Once the FASTA data is converted to TSF (Golden Helix annotation format) then it can be loaded into the GenomeBrowse plot window for visualization.

Let me know if you have any further questions.



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Asked: 2017-06-12 07:10:40 -0600

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Last updated: Aug 09 '17