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  • Cufflinks: sort order of reads in bams must be the same

    Hi all,

    I am trying to run cufflinks on STAR-aligned reads. After converting to BAM and executing "sort" command I do this:

    cufflinks -uN --GTF /path/to/reference.gtf -b /path/to/genome.fasta --compatible-hit-norm mapped_reads_sorted.bam

    However, cufflinks does not run, reporting the following:
    Error: sort order of reads in bams must be the same

    This is double-confusing, because I am only using one BAM file...

    Can someone help?

  • #2
    Remove COLONS

    Remove colons in the FASTA file and the GFF file.

    Comment


    • #3
      You must remove the colons in the FASTA reference and the GTF file. (make sure the names match up after)

      Comment

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