Hey everyone,
currently I am struggling with aligning my seq data to my reference sequence. The annotation file hasn’t any exons, just CDS, gene and region and therefore I can’t use STAR aligner. Are there any possibilities to add --sjdbGTFfeatureExon to change the feature of the annotation file??
Best,
Benedikt
Hi @benediktp
maybe consider mapping reads without gene annotation and count reads mapped to genes using featureCounts or htseq-count. Do you work with bacterial data? In this case you probably don’t need gapped aligner.
Kind regards,
Igor
The question he is asking is actually a common issue (a common problem encountered within a Galaxy instance): how to add parameters to a program? STAR has many parameters in command-line mode, but after integration into Galaxy, these parameter options are removed, making it impossible to customize settings. The user is asking about how to add the desired parameters for their already downloaded and installed software packages within Galaxy.
I think it’s just a very important question; it’s essential for personalizing a local Galaxy instance.
Hi @Naibin_Duan
The option exists in the wrapper. Try a “browser find” on the tool forms to find nested options. Most are tagged with the command-line term. Example:
To change GTF content itself as a preparation step, one could try using gffread.
For the prior Q&A, that was just advice for what seemed like a newer user, so keeping it simple and supported by tutorials was the idea behind the reply. There are of course probably N+ ways to do any particular manipulation… other Q&A at this forum covers most for Star already.
Anyone can contribute to adding more options to existing tool wrappers, or to create entirely new wrappers. If the best practices are followed, we’ll host those in the Main ToolShed. If still in development, the Test ToolShed is a sandbox. And there is always the option to host your own ToolShed for custom/private work. All work with a Galaxy instance the same way. The Docs below have wheres and how-tos.
This is Q&A from last week with some more details:
And, this is just a summary of key places where development happens that will lead to the rest: Private Galaxy Servers.
Feel free to ask questions if anything is not clear or you need help 
Matrix can be better for quick development help since it reaches the technical teams directly, but you can also start here and we can help to loop that in as needed. Ask in a new topic please.
