>
>
> 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 t
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:
"reply all" in your mail client. For discussion of
> 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 subs
Hi,
You will have to change the permission of fastqc to be executable. You
can open your terminal, log as root and change it. Open your terminal, type
sudo su, then it will ask your password. After you enter your password type
chmod 777
/root/Programs/Galaxy/galaxy-dist/tool-data/shared/jars/Fas
Hi,
I believe you have to run Fastq Groomer first to convert it to sanger
format. Then you will be able to see your dataset.
https://main.g2.bx.psu.edu/u/dan/p/fastq
Best,
Luciano
___
The Galaxy User list should be used for the discussion
g "reply all" in your mail client. For discussion of
> 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,
> pl
index files there. Anyway, why is it not creating the indexes?
> I created links to all bowtie2 executable files. If I remove bowtie 0.12.8,
> then I get a error from tophat (bowtie not installed). Is it creating the
> index with bowtie 0.12.8?
> Thank you.
>
> Luciano
>
--
*Luci
Hi,
I installed bowtie2 and when running tophat I get the following error:
Error in tophat:
[2012-06-19 14:02:39] Beginning TopHat run (v2.0.3)
---
[2012-06-19 14:02:39] Checking for Bowtie
Bowtie version:2.0.0.6
[2012-06-19
t; 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
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source
Thanks Jeremy,
I will do it before try the *de novo *assembly.
Luciano
On Fri, May 18, 2012 at 1:44 PM, Jeremy Goecks wrote:
> I find a lot of potential new genes (hundreds or thousands of reads
> aligning to regions where there is no gene annotation),
>
>
> This shouldn't be completely unexp
.
Luciano
--
*Luciano Cosme*
-
PhD Candidate
Texas A&M Entomology
Vector Biology Research Group
www.lcosme.com
979 845 1885
co...@tamu.edu
-
___
nes with
"wrong" annotation within the coding region.
Thank you.
--
*Luciano Cosme*
-
PhD Candidate
Texas A&M Entomology
Vector Biology Research Group
www.lcosme.co
Hi,
After I uploaded a couple files yesterday, I hit the storage limit
(250Gb), then I deleted 3 datasets from my history and now I can't see
anything in that history. It still says that I am using 228Gb, but I can
only access one history with ~98Gb. I try to use show deleted datasets and
it still
;(pencil icon)
>
> Next, use a tool in the group "Operate on Genomic Intervals" to compare
> these intervals for overlap. The tool "Cluster" with the option "Find" is
> mostly likely the one you will want to use.
>
> As a final step, summariz
Hi,
I was wondering if there is any tool on Galaxy were I can obtain a table
with how many reads have been mapped to a given sample and to a given gene
(for example, use a Tophat output and use a GFF file to obtain the table).
I am using HTSeq to get it (htseq-count). There is also GenomicRanges
3
<http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy#CA-78df7933c2e9e4b1411a7e60fd3087c684c79664_3>
% export PATH=~/galaxy-python:$PATH
On Sat, Feb 25, 2012 at 5:50 PM, Luciano Cosme wrote:
> *Hi Everyone,
>I have been running a Local Galaxy instance for a long time, but now I
>
*Hi Everyone,
I have been running a Local Galaxy instance for a long time, but now I
am having some problems with uploading data. I am getting the following
error:*
Can't create peek [Errno 2] No such file or directory:
'/home/koala2/galaxy-dist/database/files/000/dataset_13.dat'
*
and from the
.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
-------
Luciano Cosme
PhD Candidate
Texas A&am
Hi Lanelle,
You can go in Text Manipulation and use the "Convert delimiters
to TAB" or "Cut columns from a table" and play with it a bit until you
get your data in the format you want. I used it sometime ago to
manipulate data for other analysis, but I don't remember exactly how I
did
face at:
http://lists.bx.psu.edu/
-------
Luciano Cosme
PhD Candidate
Texas A&M Entomology
co...@tamu.edu
---
___
The Galaxy User list should be used for the discussion of
Galaxy analysis
Hi,
I have been using Galaxy for manipulation of data sets and you can
run analysis on DSAP http://dsap.cgu.edu.tw/index.htm or use miRNAkey http://ibis.tau.ac.il/miRNAkey/
. Well there are other options as well, but these are pretty easy to
use.
Luciano
On Dec 5, 2011, at 3:10 PM, sha
puter where I have
galaxy, using a ftp server seems to be a extra step. The only other
way that I thought was to upload the compressed files, but I have
around 15 files for every sample (14 sample total) and I would have to
concatenate them later on.
Thank you.
Luciano
Hi,
I am running galaxy locally and when I perform alignments with TopHat I
get the following error:
Error in tophat:
[Fri Jul 29 17:55:47 2011] Beginning TopHat run (v1.3.1)
---
[Fri Jul 29 17:55:47 2011] Preparing output location ./tophat_out/
[Fri
Hi,
I am running Galaxy locally (Ubuntu 11.04) and I am getting this error
message when I try to use mapping with bowtie:
Error indexing reference sequence
/bin/sh: bowtie-build: not found
Then I downloaded bowtie and tried to create a symbolic link using at
/bin:
ln -s /home/koala2/bowtie
24 matches
Mail list logo
