Re: [galaxy-user] Help!! Tophat paired end reads

[Carlos Borroto]

Hi Jennifer,

This is a subject I'm interested in. I wonder if you could share a
workflow to estimate percentage of reads mapping to for example
exomes(I can get the coordinates for a GFF dataset). I have a mapping
result for RNA-seq data and by looking in the browser, it seems to
also have a lot of reads mapping outside of exomes, but I would like
to put numbers on it.

Thanks,
Carlos
P.D. I'm trying now to get GATK's 'Depth of Coverage' to work, but I'm
having some issues with it. Is there any other options in Galaxy?

On Mon, Apr 16, 2012 at 12:27 AM, Jennifer Jackson j...@bx.psu.edu wrote:
 Hi Jiwen,

 The bioinformatics part of your analysis sounds as if it went fine, so that
 is good news. This list may not be the best place to get feedback about
 library construction methods, but we can see who has help to offer.

 I did a quick search myself and found this recent publication that includes
 a comparison of rRNA depletion methods with mapping profiles:
 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0027288

 Best,

 Jen
 Galaxy team


 On 4/15/12 8:24 AM, 杨继文 wrote:

 Hi,
 I am very confused by my mapping. Please help me figure out what's wrong
 with my operation.
 I got Illumina Hiseq 2000 paired end reads (mouse), and I used Tophat to
 map these reads.
 After mapping, I used IGV to have a look at the mapping.
 I can see that some of the reads fall into exons or span exons (splice
 junction). These reads seem to fit very well. However, I can also see a
 lot reads mapped to non-coding region. Are these reads from pre-mRNA? or
 my mapping was wrong? Did anybody have similar experience??
 Furthermore, I can see huge enrichment of reads in 3' UTR (much much
 more than the coding region). Is this normal? Is this caused by the rRNA
 depletion method ?
 Looking forward to your reply
 Jiwen




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 --
 Jennifer Jackson
 http://galaxyproject.org
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[galaxy-user] Cuffdiff

[Ateequr Rehman]

Dear All
I have simple and question for cuffdiff
should we run cuffdif on merge transcript file (produced by cuffmerge) and 
concatenate data sets
or directly on cufflink produced files, in the later case, i have two 
transcript files resulting from cufflink on sample 1 and 2 respectively,
result using sample 1 as transcripts are not the same when i am suing sample 2 
as transcript 


i am bit confused what should be the correct way

any help is very much welcomed

Best
ateeq

 
Ateequr Rehman
House No. 2 ground floor
Blauenstr. 10
79115 Freiburg im Breisgau___
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Re: [galaxy-user] [galaxy-dev] Create and Transfer Galaxy Page

[Jeremy Goecks]

Hi Todd,

 [Not sure if this is better suited to galaxy-dev or -user, so I'm sending 
 to both].

galaxy-user is most appropriate for this question because it related to usage 
of Galaxy; galaxy-dev is for local installation and tool development questions.

 My question is - can I create a Galaxy 'Published Page' from my local Galaxy 
 instance/histories, and then transfer that page to the main Galaxy instance?

Not currently, though this is in our long-term plan.

 The reason is that I cannot make my local Galaxy instance public, as I am 
 using a campus resource to host our galaxy.  If this is possible, how can I 
 do that?  If not, any other ideas?

It is possible to move datasets and workflows relatively easily between 
instances, so I'd recommend that:

(a) you move your data and workflows to our public instance;
(b) rerun your analyses on the public instance to create the required;
(c) create and host the Page on our public instance.

You can be assured that we will maintain our public server over the coming 
years and your Page will remain available and have a stable URL.

 Also, are there any tutorials/pages on how to create Published Pages in 
 Galaxy in the first place?

Not yet, though the idea is for the Page editor to be self explanatory. Here's 
how to get started with Pages:

(a) from User menu, go to Saved Pages;
(b) create a Page;
(c) edit the Page using the Web-based editor; there are menus for inserting 
embedded datasets, workflows, histories, and visualizations as well as 
performing standard word-processing operations.

Let us know if you have problems/questions and we'll start a guide for creating 
Pages.

Best,
J.


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