Re: [galaxy-user] miRNA-seq help

2013-10-14 Thread Jennifer Jackson 

Hi Gabriel,

SAM format is just tabular data- so you could assign that as a datatype 
(use the pencil icon). The only concern here would be the size of the 
files - Excel can be easily swapped with very large files.


Converting SAM->interval is another option, if you just need the 
coordinates. This can also be set as "tabular" format for Excel


For both, make sure the file ends in ".tab" not ".tabular" and possibly 
just "txt", once downloaded, in order for Excel to recognize it (as far 
as I know).


Galaxy will perform many of the calculations that Excel will do (see 
group "Text manipulations" & others tools like "Group" or those in 
"Statistics", but you have likely already seen those.


Best!

Jen
Galaxy team


On 10/14/13 11:13 AM, Gabriel Calvin wrote:
Thanks for the responses It appears these programs require some 
background in Python or R. Is there a less code-intensive way to 
manipulate a sam or bam into a format viewable in Excel? Does Galaxy 
provide a tool for this?


If it simply is a matter of learning code, so be it.


On Fri, Oct 11, 2013 at 3:20 PM, Gabriel Calvin > wrote:


The organism is fruit fly. The piRNA reference sequence was
obtained from http://www.fruitfly.org/p_disrupt/TE.html as
FASTA.FORMAT.v9.4.1.

I will check out those programs.

Gabriel




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Re: [galaxy-user] miRNA-seq help

2013-10-14 Thread Luciano Cosme 
Hi Gabriel,
  I believe you can do it with galaxy. I never used it for miRNA analysis
because most of the miRNAs of the organism that I work with are not
annotated on its genome. You will need the total number of reads that
uniquely map to each mature miRNA. What I have notice is that the guide and
passenger strand most of the time have huge differences in expression. To
get that your annotation file (gtf or gff) would have to have each strand,
its okay if you don't have it. Probably you can use HTseq. It is available
on the Galaxy tool shed. You can also use it directly at
http://galaxy.nbic.nl/ (it is NGS:RNA Analysis). You can also run it on
your computer http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
  After you get the counts you can use Deseq to calculate differential
expression. See if you can get the counts first. I never used the Galaxy
Deseq wrapper, but they have it on the tool shed too. You can install R and
the Deseq package on your computer. You might install RStudio as well. I
can send you the code I used to do my analysis with comments if you decide
to give it a try.
Best,

Luciano



On Mon, Oct 14, 2013 at 1:13 PM, Gabriel Calvin  wrote:

> Thanks for the responses It appears these programs require some background
> in Python or R. Is there a less code-intensive way to manipulate a sam or
> bam into a format viewable in Excel? Does Galaxy provide a tool for this?
>
> If it simply is a matter of learning code, so be it.
>
>
> On Fri, Oct 11, 2013 at 3:20 PM, Gabriel Calvin  wrote:
>
>> The organism is fruit fly. The piRNA reference sequence was obtained from
>> http://www.fruitfly.org/p_disrupt/TE.html as FASTA.FORMAT.v9.4.1.
>>
>> I will check out those programs.
>>
>> Gabriel
>>
>
>


-- 
*Luciano Cosme*

-
PhD Candidate
Texas A&M Entomology
Vector Biology Research Group
www.lcosme.com
979 845 1885
co...@tamu.edu
-
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Re: [galaxy-user] miRNA-seq help

2013-10-14 Thread Gabriel Calvin 
Thanks for the responses It appears these programs require some background
in Python or R. Is there a less code-intensive way to manipulate a sam or
bam into a format viewable in Excel? Does Galaxy provide a tool for this?

If it simply is a matter of learning code, so be it.


On Fri, Oct 11, 2013 at 3:20 PM, Gabriel Calvin  wrote:

> The organism is fruit fly. The piRNA reference sequence was obtained from
> http://www.fruitfly.org/p_disrupt/TE.html as FASTA.FORMAT.v9.4.1.
>
> I will check out those programs.
>
> Gabriel
>
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Re: [galaxy-user] miRNA-seq help

2013-10-11 Thread Gabriel Calvin 
The organism is fruit fly. The piRNA reference sequence was obtained from
http://www.fruitfly.org/p_disrupt/TE.html as FASTA.FORMAT.v9.4.1.

I will check out those programs.

Gabriel
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Re: [galaxy-user] miRNA-seq help

2013-10-11 Thread Luciano Cosme 
You can also try miRDeep_star. It identifies know miRs and discovers
possible new miRs. There is a java gui and a command line option. However
you have to get your genome indexed with a script they provide. I used
Deseq for the known miRs as well.

Luciano

Sent from my HTC One.
On Oct 11, 2013 12:19 PM, "Hoang, Thanh"  wrote:

> Hi Calvin,
> I am analyzing miRNA differential expression from my small RNA sequencing
> data from mouse tissue using Bowtie > Htseq>Deseq.
> I tried both whole mouse genome and hairpin miRNA( from miRbase) as
> reference sequences and annotation of all known miRNA (from miRbase). These
> worked for me.
> Another option is that you can try mirDeep2 and Novoalign.
> Anyway, what organism are you working with? Where u download the piRNA
> reference sequence?
> Let me know what happens
> Thanh
>
>
> On Fri, Oct 11, 2013 at 12:51 PM, Gabriel Calvin wrote:
>
>> Hi, I'm new to Galaxy and am trying to view several miRNA datasets as a
>> differential expression. The pipeline I'm using is Bowtie for Illumina
>> (paired-end run) > SAM-to-BAM > ? > xls. The references I used with Bowtie
>> are a mature miRNA fasta and a piRNA fasta and the reads are 30nt in length.
>>
>> So, my questions are: Is this the proper pipeline? How do I go about
>> converting the BAM into a xls file viewable in Excel?
>>
>> Thanks!
>>
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>> please use the interface at:
>>
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>>
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>>
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>>
>
>
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Re: [galaxy-user] miRNA-seq help

2013-10-11 Thread Hoang, Thanh 
Hi Calvin,
I am analyzing miRNA differential expression from my small RNA sequencing
data from mouse tissue using Bowtie > Htseq>Deseq.
I tried both whole mouse genome and hairpin miRNA( from miRbase) as
reference sequences and annotation of all known miRNA (from miRbase). These
worked for me.
Another option is that you can try mirDeep2 and Novoalign.
Anyway, what organism are you working with? Where u download the piRNA
reference sequence?
Let me know what happens
Thanh


On Fri, Oct 11, 2013 at 12:51 PM, Gabriel Calvin  wrote:

> Hi, I'm new to Galaxy and am trying to view several miRNA datasets as a
> differential expression. The pipeline I'm using is Bowtie for Illumina
> (paired-end run) > SAM-to-BAM > ? > xls. The references I used with Bowtie
> are a mature miRNA fasta and a piRNA fasta and the reads are 30nt in length.
>
> So, my questions are: Is this the proper pipeline? How do I go about
> converting the BAM into a xls file viewable in Excel?
>
> Thanks!
>
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
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> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
>   http://galaxyproject.org/search/mailinglists/
>
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[galaxy-user] miRNA-seq help

2013-10-11 Thread Gabriel Calvin 
Hi, I'm new to Galaxy and am trying to view several miRNA datasets as a
differential expression. The pipeline I'm using is Bowtie for Illumina
(paired-end run) > SAM-to-BAM > ? > xls. The references I used with Bowtie
are a mature miRNA fasta and a piRNA fasta and the reads are 30nt in length.

So, my questions are: Is this the proper pipeline? How do I go about
converting the BAM into a xls file viewable in Excel?

Thanks!
___
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