Question: Extracting Sequences For Transcripts From Reference Genome
0
Lizex Husselmann • 80 wrote:
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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