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  • cuffmerge fail

    Hi ,
    i am trying to use cuffmerge from Cufflinks after doing all steps in "getting started page"
    in the 3 step when i was trying to merge , i am having this error:

    [Sun Jul 31 22:53:56 2011] Beginning transcriptome assembly merge
    -------------------------------------------

    [Sun Jul 31 22:53:56 2011] Preparing output location ./merged_asm/
    Warning: no reference GTF provided!
    [Sun Jul 31 22:53:56 2011] Converting GTF files to SAM
    [22:53:56] Loading reference annotation.
    [22:53:56] Loading reference annotation.
    [Sun Jul 31 22:53:56 2011] Assembling transcripts
    You are using Cufflinks v1.0.3, which is the most recent release.
    [bam_header_read] EOF marker is absent.
    [bam_header_read] invalid BAM binary header (this is not a BAM file).
    File ./merged_asm/tmp/mergeSam_fileuL7Jzz doesn't appear to be a valid BAM file, trying SAM...
    Error: sort order of reads in BAMs must be the same
    [FAILED]
    Error: could not execute cufflinks


    how can i solve it?
    do i have to sort some files?

    thank in advance..
    Papori

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