Hello Lizex,
The primary reason why runs fail is the input data format. A double
check that the reference genome identifiers are the same between the BAM
files and any reference GTF files would be recommended. This and other
common issues are covered in our FAQ here:
Hi
I've started an alignment using the command line (Tophat v1.3.3). I've uploaded
the files (accepted.bam) onto Galaxy and upon doing the Cufflinks analysis on
the Galaxy interface, it shows an error. I had to look at the options. I've
change the options to default and run it again but still
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