February 2014 - galaxy-user - lists.galaxyproject.org

Query regarding NCBI BLAST+ blastx
by Deepak Datta 05 Feb '14

05 Feb '14

Hello, I was working with *NCBI BLAST + blastx.*. I have a question regarding one of the columns that reads 'qframe'. When we do Blast on NCBI, we get a column called query coverage. And when we perform NCBI BLAST + blastx, we get 25 columns. I wanted to know which of these columns is analogous to the "query coverage" column. And if these columns do not correspond to "query coverage" then can you kindly let me know how am I supposed to derive that? Looking forward to your response. -- *DD*

3 2

Chip-SEq S.cerevisiae IOn-Torrent
by Mónica Pérez Alegre 04 Feb '14

04 Feb '14

Hi everybody. I´m trying to analyze Chip-SEq Data from Ion-Torrent using Peak Calling/MACS. I have some questions: · How do I establish the Tag size? The median of size reads in my data are 156pb, the max 306? · Bandwidht: is the sonication size? Thanks in advance Regards ☺If you have used the Services of the Genomics Unit of Cabimer, we would be grateful if you would give us a mention in future publications Mónica Pérez Alegre, PhD Genomics Unit CABIMER-CSIC Edif. CABIMER - Avda. Américo Vespucio s/n Parque Científico y Tecnológico Cartuja 93 41092 Seville-SPAIN Tlf: +34 954 467 828 Fax: +34 954 461 664 www.cabimer.es<http://www.cabimer.es/> http://www.cabimer.es/web/es/unidades-apoyo/genomica

2 1

mpileup max coverage
by Wang, Michael 04 Feb '14

04 Feb '14

Hi All, one quick Q: how can I set max per-file depth to more than 8000 under mpileup. Thanks! Michael ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer

2 1

Installing tool in galaxy on cloud
by Malik, Shivani 03 Feb '14

03 Feb '14

Hi All, I want to use Tophat2 on amazon cloud. I could not find it in the regular tools unlike the public server. Am I using the right version? I tried installing it through admin on cloud .Though I was able to make myself admin through cloudman instance , I could not see any admin panel on Galaxy main page. What am I doing wrong?Any help is appreciated. Thanks. Shivani

2 1

remove versions of tool
by Ketan Maheshwari 02 Feb '14

02 Feb '14

Hi, I renamed my tool name in <tool name=""> but when I restart Galaxy server, I see a dropdown in front of the tool title with two versions with same value. When I select one it gives current name and when selecting other it gives the older name of the tool. My intention here was to rename the tool and I did not do anything that would tell Galaxy to preserve versions. After looking into the past mailing list posts, I tried to : 1. Restart Galaxy server. 2. Deleted integrated_tool_panel.xml 3. cleared my browser cache and cookies None of the above worked though. Any suggestions? Attached is a snapshot of what I am seeing. Best, -- Ketan

2 2

special character $ gets converted to X in tool
by Ketan Maheshwari 01 Feb '14

01 Feb '14

Hi, In a test tool that I am working on, I need to enter text preceded by a $ sign to be interpreted as an environment variable by the underlying running script. However, it seems that the $ sign gets converted to X when it gets passed to the tool executable. Is there a way to work around this or should I be doing something else to pass environment variables via Galaxy tool UI. Thanks, Ketan

3 4