[Gmod-ajax] fastq in Jbrowse

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[Gmod-ajax] fastq in Jbrowse

Chathura Gunasekara
Hi,
I am want to display fastq data in a Jbrowse. How should I proceed to implement this ?
what tools do i need to convert the data to the format required for Jbrowse ?

Thank you

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Chathura

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Re: fastq in Jbrowse

Colin
Hi Chathura,

Generally, a fastq file will represent unaligned reads, so you can first align the reads to the genome using a tool like bwa or tophat (depends on the type of sequencing the fastq represents), and then this can give you a BAM file, which JBrowse can read (generally you just drop the BAM file and BAM index file in your data directory, and then use add-bam-track.pl to create the track).

Hope that helps,


-Colin  

On Sat, Mar 26, 2016 at 1:07 PM, Chathura Gunasekara <[hidden email]> wrote:
Hi,
I am want to display fastq data in a Jbrowse. How should I proceed to implement this ?
what tools do i need to convert the data to the format required for Jbrowse ?

Thank you

--
Chathura

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140
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------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140
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