Re: [galaxy-user] get wig file after tophat

2011-04-20 Thread Ying Zhang
is email. We would be happy to help add it to Galaxy if this would be of interest to you or other Galaxy users. If there is any way we can be of assistance, please let us know! Very best wishes, Ann Loraine On 2/21/11 3:39 PM, "Ying Zhang" wrote: Hi: I am using tophat in galaxy to a

Re: [galaxy-user] how to find out the gene_ID correspond to CUFF ID

2011-03-01 Thread Ying Zhang
have limited experience in computing so I do not know how to format this file. Best Ying Quoting vasu punj : I believe you need to format the Ensemble file Chromosome columns is not correct.   Vasu --- On Tue, 3/1/11, Ying Zhang wrote: From: Ying Zhang Subject: Re: [galaxy-user] how to

Re: [galaxy-user] how to find out the gene_ID correspond to CUFF ID

2011-03-01 Thread Ying Zhang
s CUFF ID? Thank you very much! Best Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286 ___ The Galaxy User list should b

[galaxy-user] how to find out the gene_ID correspond to CUFF ID

2011-02-28 Thread Ying Zhang
Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286 ___ The Galaxy User list should be used for the discussion of Galaxy

[galaxy-user] get wig file after tophat

2011-02-21 Thread Ying Zhang
Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286 ___ The Galaxy User list should be used for the discussion of Galaxy

[galaxy-user] look for wig file

2011-02-21 Thread Ying Zhang
lot! Best Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286 ___ The Galaxy User list should be used for the discussion

[galaxy-user] (no subject)

2011-02-08 Thread Ying Zhang
for one sample, but when do tophat analysis, do I need to merge those two files into one file? do you know what is the usual parameter set up for paried-end RNA-seq analysis(with a 300 bp fragment)? Thank you very much! I really appreciate your help! Best Ying Zhang, M.D., Ph.D. Postdoctoral