When running cufflinks on my accepted_hits.bam files from tophat, I get this output, truncated as there are many CIGAR errors.
It looks like I'm having the same error as this thread was.
However, I can't get cufflinks to compile with the source changes. The dependencies fail to be noticed. I'm following the guide here http://cufflinks.cbcb.umd.edu/tutorial.html and have tried on two computers now with no luck. Is there by chance a pre-compiled version with the fix, or some other way around this issue?
Thanks for any help.
Code:
You are using Cufflinks v2.0.2, which is the most recent release. Warning: BAM header too large File accepted_hits.bam doesn't appear to be a valid BAM file, trying SAM... [12:02:25] Inspecting reads and determining fragment length distribution. SAM error on line 806: CIGAR op has zero length SAM error on line 823: invalid CIGAR operation SAM error on line 831: CIGAR op has zero length SAM error on line 847: CIGAR op has zero length SAM error on line 874: CIGAR op has zero length SAM error on line 879: CIGAR op has zero length
However, I can't get cufflinks to compile with the source changes. The dependencies fail to be noticed. I'm following the guide here http://cufflinks.cbcb.umd.edu/tutorial.html and have tried on two computers now with no luck. Is there by chance a pre-compiled version with the fix, or some other way around this issue?
Thanks for any help.
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