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 correctly is the first place to start. Click on the pencil icon for the datasets and on the 'Edit Attributes' form, scroll down to datatype, and assign if necessary.

BAM data is somewhat difficult to load or have in a history without having it detected and assigned - so that is likely a problem. But a reassignment to tabular can occur for SAM data, if you have been performing text manipulations on the data and do not have headers. Just confirm format and change the dataset assignment back to SAM so that Cufflinks will accept it as input. A metadata error (presented in a yellow box within the dataset) may be an indicator that something is wrong, although one round of 'attempt to manually correct' using the link provided is good to try and can often correct the issue.

Hopefully this helps,

Jen
Galaxy team

On 4/30/12 7:12 AM, Ateequr Rehman wrote:
Just wanted to make sure if cofflink is working or not
cufflink is not detecting my SAM or BAM files.,



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The Galaxy User list should be used for the discussion of
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