4.6 years ago by
There is only one HTseq function wrapped for Galaxy so far, but keep watching the Tool Shed, since the paper just went out (late Feb 2014). It is for use is a local/cloud Galaxy (not Main - usegalaxy.org).
To locate in the Tool Shed http://usegalaxy.org/toolshed:
- Repository 'htseq_count'
- Synopsis: Count aligned reads (SAM/BAM) that overlap genomic features (GFF)
I did not check the other public Galaxy servers, but these do change content frequently, so a review may be worth it: https://wiki.galaxyproject.org/PublicGalaxyServers. Or maybe someone running one, also running HT tool(s), will see the post and add to it!
If you are just looking for similar functions, comparing interval regions is one of the things that Galaxy does best. Look in the tool group "Operate on Genomic Intervals" and "BED Tools" for options. Nearly any file can be converted to interval format, although some of these tools work with other formats directly. If you have a specific operation/goal in mind, please ask.
Best, Jen, Galaxy team