incorporating unjoined islands from TopHat RNA-seq output

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incorporating unjoined islands from TopHat RNA-seq output

Megan
I am doing gene annotation using MAKER.  I have RNA-seq data that I am trying to incorporate using TopHat as suggested.  The tophat2gff3 script uses the junctions.bed file, which only includes islands of reads that were joined to other islands.  Is there a simple way to incorporate unjoined islands of reads?

Thanks.
Megan



     

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Re: incorporating unjoined islands from TopHat RNA-seq output

Carson Hinton Holt
Re: [maker-devel] incorporating unjoined islands from TopHat RNA-seq output Try processing the tophat output with cufflinks and then concatenating the cufflinks GFF3 to the tophat GFF3.  You convert cufflinks output using cufflinks2gff3 script.  Cufflinks will link together the islands and junctions in the TopHat produced sam file into longer transcript like models.

Carson

On 9/8/10 11:04 AM, "Megan" <hedgyx@...> wrote:

I am doing gene annotation using MAKER.  I have RNA-seq data that I am trying to incorporate using TopHat as suggested.  The tophat2gff3 script uses the junctions.bed file, which only includes islands of reads that were joined to other islands.  Is there a simple way to incorporate unjoined islands of reads?

Thanks.
Megan



     

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