Hello Alicia,
There are two tools in the main Galaxy Tool Shed
(http://toolshed.g2.bx.psu.edu/) that would likely be helpful. Read the
input requirements for each to decide which is a better fit. Search for
'deseq' to find them:
deseq_and_sam2counts
deseq_hts
To use these tools, a local
Hi all,
I'm about to start doing gene expression analysis but i don't have a
reference genome.
I got my sequences from Illumina and i did my assemblies with CLC bio.
I was planning to use DESeq for the analysis but for that i need my gene
expression count values.
There is any tool in Galaxy that i
Since the pictures are too big for the mailling list. I will upload it in
seperate emails.
Dear all,
I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially
expressed transcripts and differentially expressed genes. In these two lists, I
would like to see the gene name, gene
Hi
Thank you! yes, your guess is correct. Now it works.
Sumathy
On May 7 2011, Jeremy Goecks wrote:
Sumathy,
It sounds like you're on the right track. To visualize data for a custom
build in Trackster, you need to create a custom build and use that in
Trackster:
(1) using the top
Sumathy,
It sounds like you're on the right track. To visualize data for a custom build
in Trackster, you need to create a custom build and use that in Trackster:
(1) using the top tabs in Galaxy, go to User --> Custom Builds;
(2) add a new build with the length info as follows:
Important not
Thanks Jim,
Vasu
--- On Fri, 5/6/11, Jim Robinson wrote:
From: Jim Robinson
Subject: Re: [galaxy-user] RNA seq analysis
To: "vasu punj"
Cc: "Austin Paul" , "Sean Davis" ,
"galaxy-user@lists.bx.psu.edu" ,
"puvan...@umn.edu"
Date: Friday,
great work but How hard is to include index
functionality with in IGV. I know we can use sam tools also but just for
convinence if it is not that much of work.
Vasu
--- On Fri, 5/6/11, Sean Davis wrote:
From: Sean Davis
Subject: Re: [galaxy-user] RNA seq analysis
To: "Austin Paul&quo
Hi
I may be doing in a wrong way. I clicked trackster and I added the custom
build genome. Since it is a very small genome (~2kb), I considered this as
a single contig. Then I cliked "add tracks" and added my data file. But I
got a message "no data for this contig. Whenever I used built in g
have been using IGV 2 beta version it is great work but How hard is
to include index functionality with in IGV. I know we can use sam
tools also but just for convinence if it is not that much of work.
Vasu
--- On Fri, 5/6/11, Sean Davis wrote:
From: Sean Davis
Subject: Re: [galaxy-use
Sumathy,
What kind of problems are you having with Trackster?
J.
On May 6, 2011, at 8:30 PM, wrote:
> Hello
>
> I was able to run RNA seq data against a custom build genome. How can I
> visualize the results. I tried via trackster and unfortunately I couldn't.
> Can you help me?
>
>
> Tha
convinence if it is
not that much of work.
Vasu
--- On Fri, 5/6/11, Sean Davis wrote:
From: Sean Davis
Subject: Re: [galaxy-user] RNA seq analysis
To: "Austin Paul"
Cc: "galaxy-user@lists.bx.psu.edu" ,
"puvan...@umn.edu"
Date: Friday, May 6, 2011, 8:02 PM
IGV
I generally take the GTF file to UCSC genome browser.
If you are visualizing Bam file after alignment. I found IGV convinenet, though
you may be able to visualize in Galaxy.
Vasu
--- On Fri, 5/6/11, puvan...@umn.edu wrote:
From: puvan...@umn.edu
Subject: Re: [galaxy-user] RNA seq analysis
Oops. Good to know. Thanks.
Austin
On Fri, May 6, 2011 at 6:02 PM, Sean Davis wrote:
> IGV reads BAM files just fine; no need to convert to SAM.
>
> Sean
>
> On Fri, May 6, 2011 at 8:45 PM, Austin Paul wrote:
>
>> There are many ways. I typically use IGV. It needs a sam file, so I
>> first
IGV reads BAM files just fine; no need to convert to SAM.
Sean
On Fri, May 6, 2011 at 8:45 PM, Austin Paul wrote:
> There are many ways. I typically use IGV. It needs a sam file, so I first
> convert the bam to sam in galaxy, then download the sam file. In IGV, I
> upload the reference and t
There are many ways. I typically use IGV. It needs a sam file, so I first
convert the bam to sam in galaxy, then download the sam file. In IGV, I
upload the reference and the sam file, then use IGVtools to index the sam
file, then I can visualize the data.
Austin
On Fri, May 6, 2011 at 5:30 PM,
Hello
I was able to run RNA seq data against a custom build genome. How can I
visualize the results. I tried via trackster and unfortunately I couldn't.
Can you help me?
Thanks
Sumathy
___
The Galaxy User list should be used for the di
Hi Austin
I did all these (grooming and trimming)on rna-seq data and I don't have a
problem with built in genome . I'll try again!
Thanks
Sumathy
On May 6 2011, Austin Paul wrote:
Hi,
You need to run fastq groomer on your rna-seq data. Your reference is fine
as a fasta.
Austin
On
Hi,
You need to run fastq groomer on your rna-seq data. Your reference is fine
as a fasta.
Austin
On Fri, May 6, 2011 at 10:26 AM, wrote:
>
> Hi David,
>
> Thanks!When I tried to run Tophat, it doesn't recognise my FASTA file and
> it says "History does not include a dataset of the required f
Hi David,
Thanks!When I tried to run Tophat, it doesn't recognise my FASTA file and
it says "History does not include a dataset of the required format /
build". Do you have any thoughts about this?
Now it makes more sense about "multihits". Thanks for sharing your
workflow.
With regards
Hi,
I have done exactly the same kind of thing for adenovirus so I can help with
it. In answer to question 1 you do not need to index it will be done for you
when tophat is called. Secondly you should leave the 40 multihits as it is and
post analysis filter out the multihits - this will allow y
Hi
I have a couple of questions regarding RNA seq analysis. My questions are
1.I need to use a viral genome (very small, ~2kb ) as a reference genome
and it is not available in Galaxy. I guess I can use this data from my
history. I have a fasta file but I am not sure whether I have to do some
Hello,
On 4/28/11 9:21 PM, puvan...@umn.edu wrote:
I am new to Galaxy and I am not sure whether these topics were discussed
earlier. I followed the steps up to cufflinks and I did not have any
problems. Thanks for the RNA seq tutorial. My questions are
1. How do I know the number of reads mapped
I am new to Galaxy and I am not sure whether these topics were discussed
earlier. I followed the steps up to cufflinks and I did not have any
problems. Thanks for the RNA seq tutorial. My questions are
1. How do I know the number of reads mapped against the reference genome
used after Top Hat ma
ail address.
Thanks,
David
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Thursday, April 07, 2011 3:42 PM
To: David K Crossman
Cc: galaxy-user
Subject: Re: [galaxy-user] RNA seq analysis and GTF files
David, can you please share your history with me and I'll take a look (H
t before moving on). Any info, suggestions or help
would be greatly appreciated.
Thanks,
David
-Original Message-
From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu
] On Behalf Of Jeremy Goecks
Sent: Friday, April 01, 2011 8:47 AM
To:
Cc: gala
[mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jeremy Goecks
Sent: Friday, April 01, 2011 8:47 AM
To:
Cc: galaxy-user
Subject: Re: [galaxy-user] RNA seq analysis and GTF files
On Mar 31, 2011, at 12:30 PM,
mailto:ssa...@ccib.mgh.harvard.edu>>
mailto:ssa...@ccib.mgh.
On Mar 31, 2011, at 12:30 PM,
wrote:
> Hi Jeremy,
> I used your exercise to perform an RNA-seq analysis. First I encountered a
> problem where the gene IDs were missing from the results. Jen from the Galaxy
> team suggested this:
>
> "Yes, the team has taken a look and there are a few t
HI Jeremy,
Thanks for the feedback. I know what you mean about tophat not having the same
functionality of bowtie. However, I think whatever tophat does do (now or in
the future) I think it is useful to collect the multihits separately since
either you leave them in and over estimate gene expre
Hello,
I like your approach of running the alignment tools with liberal settings
and then filtering the results into different categories.
This discussion reminds me of how in expression microarray analysis, we face
uncertainty as to what molecules (exactly) are hybridizing to the probes on
a chi
Thanks Ann for your comments and for the stuff you showed at IGB - looks very
interesting. I agree that multihits may the equivalent of the problem you
describe from microarrays. I think, for me anyway, knowing the scale if the
issue is the key thing at this stage. As you imply from your email t
Hello,
I like your approach of running the alignment tools with liberal settings
and then filtering the results into different categories.
This discussion reminds me of how in expression microarray analysis, we face
uncertainty as to what molecules (exactly) are hybridizing to the probes on
a ch
--- On Wed, 2/23/11, Jeremy Goecks wrote:
From: Jeremy Goecks
Subject: Re: [galaxy-user] RNA seq analysis
To: "David Matthews"
Cc: galaxy-u...@bx.psu.edu
Date: Wednesday, February 23, 2011, 10:05 PM
Hi David,
This is a really interesting workflow. My comments:
(1) I encourage you
Hi David,
This is a really interesting workflow. My comments:
(1) I encourage you to start a discussion about this idea on seqanswers.com;
you'll reach more people and may have a better discussion there. Ideally,
you'll get a Tophat developer to chime in on what I perceive to be the main
issue
Hi all,
Further to my last email, I've published a workflow (Bristol workflow )
which does what I described below - hope this helps in understanding what I'm
on about (!).
Best Wishes,
David.
On 23 Feb 2011, at 14:41, David Matthews wrote:
> Hi Jeremy,
>
> I thought I'd write to get a
Hi Jeremy,
I thought I'd write to get a discussion of a workflow for people doing RNA seq
that I have found very useful and addresses some issues in mapping mRNA derived
RNA-seq paired end data to the genome using tophat. Here is the approach I use
(I have a human mRNA sample deep sequenced wit
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