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|06-09-2015, 03:54 AM||#1|
Join Date: Oct 2010
Cufflinks: sort order of reads in bams must be the same
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?
|bam file, cufflinks, sorting|