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.
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
☺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
Edif. CABIMER - Avda. Américo Vespucio s/n
Parque Científico y Tecnológico Cartuja 93
Tlf: +34 954 467 828
Fax: +34 954 461 664
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.
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.
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.