Hi Sara, Starting with the assembled transcripts GTF file from Cufflinks, the following will pull out complete fasta records for each: 1 - "Filter and Sort -> Filter" using condition " c3!='transcript' " This removes lines that are technically out of spec for GTF format (thanks goes to Jeremy for the workaround). 2 - Send the resulting filtered GTF file to the "Fetch Sequences -> Extract Genomic DNA" tool and use the options 'Interpret Features' = True and 'Output data type' = Fasta Best, Jen Galaxy team On 8/23/12 1:41 PM, Hanson, Sara J wrote:

Hi All,

I have mapped RNA-Seq reads to an unannotated partial genome assembly and assembled them into transcripts using the Tuxedo pipeline. II have used the "Extract Genomic DNA" tool to pull the annotated genes out of the genome assembly, but I would like the spliced transcripts as well. Is there a tool or pipeline that can retrieve the exons individually and concatenate them if they are part of the same gene? Any help on this would be much appreciated.

Thanks!

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