Hello Di Nguyen,
Without seeing your history, my initial guess is that the SAM output
from the mapping runs need to be sorted before running Cufflinks.
(Tophat, which is designed to map spliced RNA-seq data, sorts the SAM
output as part of the data processing, but BWA and Bowtie do not).
Hello Ateequr,
To confirm, you are working on the main public Galaxy instance at:
http://usegalaxy.org (https://main.g2.bx.psu.edu/)?
There are at present no known problems with Cufflinks. If your datasets
are not recognized by the tool, then a double check that the datatype is
assigned
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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