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  • cuffmerge problems

    Hello
    I'm founding some problems with cuffmerge
    I've a fasta file of 27 supercontigs from broad institute, which I edited to this format
    >Supercontig_1.1

    I've downloaded also the gtf file from Broad
    As an example, the first lane is
    Supercontig_1.1 CNB1_FINAL_CALLGENES_3 start_codon 5909 5911 . - 0 gene_id "CNBG_0001"; transcript_id "CNBG_0001T0";

    I ran bowtie-build, tophat and cufflinks on my fastq files and everything is fine
    However, when I run cuffmerge, I got the message:
    You are using Cufflinks v1.3.0, which is the most recent release.
    Warning: couldn't find fasta record for '>Supercontig_1.1'!
    Warning: couldn't find fasta record for '>Supercontig_1.10'!
    Warning: couldn't find fasta record for '>Supercontig_1.11'!

    Moreover, I got a merged gtf file with 2 entries for the same sequence. For example:

    >Supercontig_1.1 Cufflinks exon 13250 13293 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "CNBG_0004"; oId "CNBG_0004T0"; nearest_ref "CNBG_0004T0"; class_code "="; tss_id "TSS1";

    Supercontig_1.1 Cufflinks exon 13233 13293 . + . gene_id "XLOC_006239" transcript_id "TCONS_00006365" exon_number "1" oId "CUFF.148.1" class_code "u" tss_id "TSS6299"

    I noted that in the first case, a ">" commes before the Supercontig. So I replace every entry in gtf adding or reoving the ">" before the "Supercontig"
    Nothing worked.
    Any clues?
    Thanks
    Charley

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