[galaxy-user] symbolic link to bowtie

2011-07-27 Thread Luciano Cosme
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

[galaxy-user] TopHat

2011-08-01 Thread Luciano Cosme
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/

[galaxy-user] Local instance data upload

2011-10-27 Thread Luciano Cosme
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 Cosme

Re: [galaxy-user] small RNA analysis

2011-12-05 Thread Luciano Cosme
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,

Re: [galaxy-user] about ftp setting up

2011-12-15 Thread Luciano Cosme
/ --- Luciano Cosme PhD Candidate Texas AM Entomology co...@tamu.edu --- ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features

Re: [galaxy-user] Performing operations on tab delimited text files

2011-12-16 Thread Luciano Cosme
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

[galaxy-user] Data not uploading in Local instance

2012-02-25 Thread Luciano Cosme
*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

Re: [galaxy-user] Data not uploading in Local instance

2012-02-26 Thread Luciano Cosme
%20Galaxy#CA-78df7933c2e9e4b1411a7e60fd3087c684c79664_3 % export PATH=~/galaxy-python:$PATH On Sat, Feb 25, 2012 at 5:50 PM, Luciano Cosme cosme.sim...@gmail.comwrote: *Hi Everyone, I have been running a Local Galaxy instance for a long time, but now I am having some problems with uploading data

[galaxy-user] Blast2GO local instance Re: Table with gene count reads

2012-03-23 Thread Luciano Cosme
likely the one you will want to use. As a final step, summarize the data by feature using the tool Join, Subtract and Group - Group. Hopefully this helps, Best, Jen Galaxy team On 3/19/12 4:36 PM, Luciano Cosme wrote: Hi, I was wondering if there is any tool on Galaxy were I can

[galaxy-user] Extract data and new genes

2012-05-18 Thread Luciano Cosme
. Luciano -- *Luciano Cosme* - PhD Candidate Texas AM Entomology Vector Biology Research Group www.lcosme.com 979 845 1885 co...@tamu.edu

Re: [galaxy-user] problems with the uploading

2012-06-06 Thread Luciano Cosme
Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- *Luciano Cosme* - PhD Candidate Texas AM Entomology Vector Biology Research Group www.lcosme.com 979 845 1885 co...@tamu.edu

[galaxy-user] Tophat and Bowtie2

2012-06-19 Thread Luciano Cosme
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

Re: [galaxy-user] Tophat and Bowtie2

2012-06-19 Thread Luciano Cosme
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 -- *Luciano Cosme* - PhD Candidate Texas AM Entomology Vector Biology Research Group

Re: [galaxy-user] Include a data folder into Galaxy

2012-06-25 Thread Luciano Cosme
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 AM Entomology Vector Biology Research Group www.lcosme.com 979 845 1885 co...@tamu.edu

Re: [galaxy-user] Data from history now showing up in fastq drop down

2012-07-06 Thread Luciano Cosme
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

Re: [galaxy-user] Permission denied error when running fastqc

2012-07-06 Thread Luciano Cosme
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

Re: [galaxy-user] How much FPKM can be take into consideration when compare gene expression

2012-09-20 Thread Luciano Cosme
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/ -- *Luciano Cosme* - PhD Candidate Texas AM

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

Re: [galaxy-user] miRNA-seq help

2013-10-14 Thread Luciano Cosme
, Oct 11, 2013 at 3:20 PM, Gabriel Calvin gac4...@gmail.com 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