Hi all,
I've been having trouble running my Arabidopsis thaliana NGS pipeline in 
galaxy. Specifically, tophat alignment to the built-in-index worked fine 
(visual assessment in IGV) but I couldn't get cufflinks/Cuffduiff to run using 
the same annotation.gtf file I'd used in the alignment. 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 SmithUniversity of York, UK                                           
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

Reply via email to