[galaxy-user] How to get reads counts from cufflins?

2012-02-08 Thread Li, Jilong (MU-Student) 
Hi all,



I got the normalized values (FPKM) from cufflinks. And I want to get relative 
reads counts. How can I do that?



Another question: how does cufflinks handle isoform genes while calculating the 
reads counts?  Or what papers can help me understand this?



Thank you very much!



Victor
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Re: [galaxy-user] How to get reads counts from cufflins?

2012-02-08 Thread Li, Jilong (MU-Student) 
Dear Jeremy,



Sorry, I didn't expressed my question clearly. I got the FPKM normalized values 
for each gene from cufflinks. And I want to get the original reads counts that 
were not normalized from cufflinks. Could you please tell me how to get those?



Thank you very much!



Victor












From: Jeremy Goecks [jeremy.goe...@emory.edu]
Sent: Thursday, February 09, 2012 4:00 AM
To: Li, Jilong (MU-Student)
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] How to get reads counts from cufflins?

Victor,

I got the normalized values (FPKM) from cufflinks. And I want to get relative 
reads counts. How can I do that?

It's not clear to me what you're looking for. FPKM is a normalized read count 
metric where the F stands for fragment, which is a single read (or half of a 
paired read).

Another question: how does cufflinks handle isoform genes while calculating the 
reads counts?  Or what papers can help me understand this?

Expectation maximization is used to probabilistically assign reads to isoforms. 
See the Cufflinks documentation for details and paper links:

http://cufflinks.cbcb.umd.edu/

Best,
J.
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[galaxy-user] about Mapping Quality

2012-02-07 Thread Li, Jilong (MU-Student) 
Hi all,

I used TopHat to map RNA-Seq reads to genomes. In the output (.sam) file, the 
value of some mapping quality (the 5th column) is 255. What does it mean? And I 
found these reads which have mapping quality 255 mapped to unique place.

Thanks!

Victor
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Re: [galaxy-user] how to transfer gene id into protein id

2011-10-28 Thread Li, Jilong (MU-Student) 
Hi,

I have some refseq gene id, like NM_* and NR_**.

I know how to transfer NM_** into protein ID NP_*. But, how to transfer 
NR_* into protein id, like NP_? I do not know. Could you please tell me?

Thank you very much!

Victor





From: Jennifer Jackson [j...@bx.psu.edu]
Sent: Thursday, October 27, 2011 11:23 PM
To: Li, Jilong (MU-Student)
Cc: galaxy-u...@bx.psu.edu
Subject: Re: [galaxy-user] how to transfer gene id into protein id

Hello,

If the reference genome is in UCSC and has a RefSeq track, then you can
extract a file with the transcript and protein identifiers from the
Table Browser called refLink and subset it for rows in your query
RefSeq transcript identifiers.

If the RefSeq data is at BioMart or another source, a similar path to
the one I outline below will work with some modifications, it all
depends on the file format, but Galaxy's tools can manipulate data is
just about every way you will need.

Using a transcript identifier query, subset protein identifiers in a
UCSC RefSeq track:

A.
Load your list of NM* identifiers (Get Data - Upload).
- set the file format to tabular (use pencil icon to Edit
Attributes - Change data type) if needed.

B.
Load RefSeq id mapping data with Get Data - UCSC Main and set the
form parameters as needed, choosing the track RefSeq Genes and the
table refLink. Make sure the region is the entire genome. Send to
Galaxy formatted as-is (tabular).

B.
Next, cut columns 3 and 4 out of the table with tool Text Manipulation
-Cut and the options c3,c4.

C. OPTIONAL, if you want the full list of coding RefSeqs for another
purpose... remove the non-coding RefSeqs with the tool Filter and Sort
- Select and the options that: NOT Matching and the pattern:
^NR_.*$. Be sure to enter the regular expression '^NR_.*$' without any
quotes.

D. Perform a join using Join, Subtract and Group - Compare two
Datasets with the options:
 - Compare: file of trans and prot id, filtered or not
 - Using column: c1 where c1 is the trans ids
 - against: file of trans ids
 - and column: c1 where c1 is the trans ids
 - To find: Matching rows of first dataset

E.
Result dataset is a two column tabular file:
transcript id tab protein id


Hopefully this helps you and others who are doing a similar task. If you
think you will be doing this a lot, be sure to consider extracting the
steps into a workflow.

Thanks for using Galaxy,

Jen
Galaxy team



On 10/27/11 1:34 PM, Li, Jilong (MU-Student) wrote:
 Hi,

 I have some refseq gene id, like NM_*.

 How can I transfer these gene id into protein id, like NP_?

 Thank you very much!

 Victor


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 please use the interface at:

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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support



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[galaxy-user] how to transfer gene id into protein id

2011-10-27 Thread Li, Jilong (MU-Student) 
Hi,

I have some refseq gene id, like NM_*.

How can I transfer these gene id into protein id, like NP_?

Thank you very much!

Victor
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[galaxy-user] FW: one error while installing galaxy

2011-10-21 Thread Li, Jilong (MU-Student) 
Hi,

When I installed galaxy, one error message appeared, which said that

ImportError: No module named distutils.util
Fetch failed.

Could you tell me how to solve this problem?
Thank you very much!
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[galaxy-user] one error while installing galaxy

2011-10-19 Thread Li, Jilong (MU-Student) 
Hi,

When I installed galaxy, one error message appeared, which said that

ImportError: No module named distutils.util
Fetch failed.

Could you tell me how to solve this problem?
Thank you very much!
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