Dear Galaxy community

I'm new to galaxy and would like to ask the following:
I have trimmed, QC'ed my data received from Illumina HiScan SQ, paired and 
single end data. Mapped using Tophat, run cufflinks, cuffmerge and cuffdiff. I 
would like to analyze the gene_exp.diff file by extracting the significant 
transcripts. I've used grep "yes" to extract only the significant transcripts. 
From this info I have the locus start and end coordinates of each transcript 
for example "XLOC_000544    XLOC_000544    -    chr1:12763969-12765675    C0    
C4    OK    3.16487    1628.25    9.00696    -4.57022    4.8722e-06    
0.00905256    yes". 
How can I go about to extract this information/or sequence from the reference 

Kind regards

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