I wanted a help. I m doing a expression analysis by using galaxy pipeline.at the last step of cufflink when i upload Sam file and gff file and run the tool .but after some time running was stopped and file showed in red colour. i have attached a picture too. Please can someone let me know what i have to do for solving this problem.
Welcome, @Iqra_azam
First, check the job output logs to see if you have a message there that is explaining more about why the job failed. This guide points to the FAQ with instructions about where to find your job logs in the application. We might be able to help more too, if you share more of these details.
The Cufflinks tool is expecting certain content in your input files, so you might find a message about which is the problem in the logs. Then you can compare your data to the Help on the tool form to see if you can notice and fix the data problem. In general these tools work in Galaxy the same as they would anywhere else, so any guides or tips or publications you find at other places would apply here, too.
We have a lot of help at our archived forum about Cufflinks if you want to see the kinds of data problems people had before that we helped with. You could even run a new search at the Hub with your error message to narrow down the hits.
And, if you would like to try using current methods and updated tools to process your data instead, we have several tutorials that you could follow. Each includes a workflow, too, that can be imported and customized.
Not to overwhelm you too much, but these are some good entry points into the tutorials for transcriptomics!
- Transcriptomics / Tutorial List
- One good place to start. → Hands-on: Reference-based RNA-Seq data analysis / Reference-based RNA-Seq data analysis / Transcriptomics
- This is another, and it is probably closest to what you are doing now. → Hands-on: De novo transcriptome reconstruction with RNA-Seq / De novo transcriptome reconstruction with RNA-Seq / Transcriptomics
- Prior training path from a recent event. It is now over but all the resources are still online and available. You can come back here to ask questions. → Transcriptomics
Let’s start there, thanks! 