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  • moriah
    started a topic cufflinks won't read my GTF file

    cufflinks won't read my GTF file

    Hi all,

    I am trying to run cufflinks and cuffdiff with an annotation file (GTF)
    I've been trying to use a file that I downloaded from the ucsc by creating a table with the needed information and sending it to galaxy.
    Now I would like to use it on my pc (not on galaxy) and I keep on getting this error :
    "Error: cannot open reference GTF file miranno.gtf for reading"

    The annotation file has full permissions to all users ...

    and it looks like this:

    chr1 hg18_wgRna exon 1092347 1092441 960.000000 + . gene_id "hsa-mir-200b"; transcript_id "hsa-mir-200b";
    chr1 hg18_wgRna exon 1093106 1093195 960.000000 + . gene_id "hsa-mir-200a"; transcript_id "hsa-mir-200a";
    chr1 hg18_wgRna exon 1094248 1094330 960.000000 + . gene_id "hsa-mir-429"; transcript_id "hsa-mir-429";
    chr1 hg18_wgRna exon 3467119 3467214 480.000000 - . gene_id "hsa-mir-551a"; transcript_id "hsa-mir-551a";
    chr1 hg18_wgRna exon 9134314 9134423 480.000000 - . gene_id "hsa-mir-34a"; transcript_id "hsa-mir-34a";
    chr1 hg18_wgRna exon 19096152 19096229 480.000000 - . gene_id "hsa-mir-1290"; transcript_id "hsa-mir-1290";
    chr1 hg18_wgRna exon 21187394 21187512 480.000000 - . gene_id "hsa-mir-1256"; transcript_id "hsa-mir-1256";
    chr1 hg18_wgRna exon 26753620 26753671 960.000000 + . gene_id "hsa-mir-1976"; transcript_id "hsa-mir-1976";

    What might be the problem?

    Thanks in advance !

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