Re: [galaxy-user] Extract sequences from [gtf file] + [genome FASTA file]

2011-05-12 Thread Edge Edge
Hi, I just read through the post at the following link, http://lists.bx.psu.edu/pipermail/galaxy-user/2011-February/001934.html I'm facing the same problem as well. I'm desired to extract out the assembled transcript by Cufflink. Can I know that how I link my output file from Tophat and Cufflink

Re: [galaxy-user] Galaxy Help: Extract sequences from [gtf file] + [genome FASTA file]

2011-05-12 Thread Jeremy Goecks
Edge, Please send questions like this to the galaxy-user mailing list, where many people see your email and can help you and/or benefit from it. I've cc'd the list for this reply. The thread you linked to is out of date. To get sequences for the features in a GTF file, you can use the 'Extract

Re: [galaxy-user] Stastistics _q valu

2011-05-12 Thread Jennifer Jackson
Hi Vasu, Would you be able to share a history link? You can email to me directly and I can share with team if needed. Thanks! Jen Galaxy team On 5/9/11 7:58 PM, vasu punj wrote: I am trying to use stat function of Galaxy, and compute q value from p values. it is giving following errors: An

Re: [galaxy-user] SNP annotation

2011-05-12 Thread Jennifer Jackson
Hello Oliver, You can compare SNP datasets using the tools under "RGENETICS" and "Human Genome Variation". dbSNP and 1000 Genomes data are locally cashed in our Libraries, making them easy to load into a history and use. Also, here is an example workflow that includes sample SNP analysis (db