Question: Problems with the annotation tool on cufflinks
gravatar for jcoelhosilveira
3.4 years ago by
jcoelhosilveira0 wrote:

Once I select the tab to have a annotation reference, the little link doesn't open and I can not add my annotated sequence. How can I solve it. Also, the program is not recognizing my .gtf sequence, somebody having the same problem?


fastq tool gtf cufflinks input • 844 views
ADD COMMENTlink modified 3.4 years ago by Jennifer Hillman Jackson24k • written 3.4 years ago by jcoelhosilveira0
gravatar for Jennifer Hillman Jackson
3.4 years ago by
United States
Jennifer Hillman Jackson24k wrote:


Tools not recognizing input either means that the datasets in the history do not have the correct metadata assignment of "database", "format", or occasionally other attributes such as the proper availability of a native/custom build reference genome on the Galaxy server or in your account.

The sequence data input should be in "fastqsanger" format - a specific type of fastq data.

The reference annotation data input should be in either "gtf" or "gff3" format (where the gff3 does not include the sequence, just the annotation lines).

I am not sure if you are using a custom reference genome or not, but if so, you can create a "custom build" (User -> Custom Builds), in order to assign it as a "datatype". Just use the custom genome in "fasta" format for the reference genome assignment on the tool form.

Some links and example tutorials to help:

This may seen like many places to look for a problem, but it is important to make sure all inputs are correctly set up in order to have the analysis produce useable results. Plus, each section is short - you should be able to locate where the inputs are "off" for your particular case and make the adjustments needed. Skip the sections that do not apply to your specific usage.

Hopefully this helps to sort out the issues! Jen, Galaxy team

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by Jennifer Hillman Jackson24k
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