[galaxy-user] help

2012-10-21 Thread Jennifer Jackson 

Hello Pranathi,

Sorry that you are having problems. Instead, use this Galaxy tool and 
the links directly between Galaxy and SRA to add the fastq data to your 
history:


1 - Get Data - EBI SRA ENA SRA

2 - Enter SRR192339 into the query box and click on search

3 - At the far right in the bottom table, under the Fastq tab, find a 
column named Galaxy, and under it a link for this data Fastq file#1. 
Click on this, and the dataset should start loaded into the current 
active history.


When you import data, be sure to note the other information about the 
experiment on the SRA form, so that you will know how to prepare the 
data for use in Galaxy. Note that you cannot load HTML data into Galaxy, 
so the index itself cannot be transferred directly. However you could 
copy and paste this into a plain text file (plain .txt, not .html), and 
upload that, if you wanted to keep a tracking history with the data.


This particular data was generated by the Illumina Genome Analyzer IIx 
technology, which creates data that is compatible with .fastqsanger 
format in Galaxy. It is also single end. This simplifies the data prep - 
simply assign the datatype as .fastqsanger and it is ready to use with 
tools. Starting with FastQC is generally considered a good idea.


Good luck with your project,

Jen
Galaxy team

ps: Please note the corrected mailing list address galaxy-u...@bx.psu.edu.
http://wiki.g2.bx.psu.edu/MailingLists


On 10/19/12 11:31 PM, pranathi pappu wrote:

  Dear Sir /Madam ,


  I have been i have been trying to upload  NGS Datasets from NCBI protein
 database onto the Galaxy website so that i could go on with my
work  but then i have been getting a result like this :
 33: SRR192339.sra
 empty
 format: txt, database:
 ?https://main.g2.bx.psu.edu/datasets/543f7c4f13f23152/edit
 Info: The uploaded binary file contains inappropriate content

 This has been the case with almost all the files that i have been
trying to
 upload . Please help me with this and i would be greatful if you
could direct me to the right person who can help me sort this matter out .
 Thanking you
 Pranathi Pappu


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

2012-10-21 Thread Xiefan Fang 
Dear galaxy users,
We have done deep sequencing on some known genomic loci using
Hiseq2000. I have already mapped the reads to the reference sequences by
using Galaxy. In the next step, I want to find SNPs and calculate the SNP
percentage within the reads. There are 500,000 to 1,000,000 reads per
biological sample. Can I do it with galaxy? If not, is there other programs
available in windows? Considering that I am not very familiar with
programming.

Thanks,
 Xiefan
University of Florida
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[galaxy-user] Fastq to Bam conversion on paired end reads picard

2012-10-21 Thread Kevin L 
Hi
I was trying to enter the 2nd fq file into the second dialog box for this
tool but then the selection automatically changes to be the same as the
filename in the first dialog.

is this a known issue?

NGS: Picard (beta)
 CONVERSION
FASTQ to BAMhttps://main.g2.bx.psu.edu/tool_runner?tool_id=picard_FastqToSam
creates
an unaligned BAM file
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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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use the Galaxy Development list:

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please use the interface at:

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