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 genome.
Kind regards
Lizex
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