Hello Weimin, The majority of issues user's encounter with RNA-seq tools is related to the inputs, so troubleshooting format is the first step. Please see the section "Example: unexpected results with RNA-seq analysis tools" here: http://galaxyproject.org/wiki/Support#Unexpected_scientific_result However, if after reviewing, you think that there may be a problem with the Cufflinks tool itself as wrapped in Galaxy, please send a bug report from the failed dataset as explained here: http://galaxyproject.org/wiki/Support#Error_from_tools Hopefully this helps, Best, Jen Galaxy team On 12/8/11 8:21 AM, dongdong zhaoweiming wrote:

Hi, I used the cufflinks to assemble my SAM file, but the results showed some CUFF's status in not "OK",it's FAIL, so that means these CUFF's corresponding sequence could not used or else mean? Thanks a lot! Reards weimin zhao

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