Error message =
Error running cufflinks. return code = -11
cufflinks: /lib64/libz.so.1.
Cufflinks/cuffdiff
would run without the annotation file and give a
differential expression output but without the annotation
file the gene_id was meaningless (XLOC_000001 etc) and all I
had was a locus for a region with differential expression.
After a lot of frustration I re ran the alignment using a
custom built genome and annotation file from Illumina:
http://cufflinks.cbcb.umd.edu/igenomes.html and hey presto,
cufflinks/cuffdiff work fine.
I
did try altering using both chr1 and 1 for chromosome name
as a discord between the chromosome naming seemed to
frequently be a problem. Apart from this, what other
reasons could there be for the built-in-index not working
with annotation.gtf files? Is this an issue with the built-in-index (Mouse-ear
Cress (Arabidopsis thaliana):
Arabidopsis_thaliana_TAIR10)?
Cheers,
Tom Smith
University of York, UK
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