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  • Confused
    Junior Member
    • Apr 2013
    • 1
    #1

    Reading BAM files in Galaxy

    Hi,

    1) I'm total a novice in this space.

    2) I'm trying to download/read the contents of the data cited here
    http://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE34740 specifically GSE34740_K562_align_b_1_GSM854404.bam

    3) I created an account so I can use Galaxy

    4) I uploaded the BAM file

    5) I ran Cufflinks hoping to extract a list of gene names and FPKM values

    6) Only the data headers were output. It looks like some kind of problem with the file format?

    7) I ran the auto-detect for file format but that didn't changes things.

    8) Any ideas?
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