Gema,

Are you issues with getting data into the correct format resolved? I see that Dan and others provided all of the help, but the times that these all posted along with your posts varied and there are a few threads, so I wanted to be sure you had what you needed.

To be clear - you will need to submit data with "fastqsanger" format to the mapping tool. If you only have fasta, then using the tool "NGS: QC and manipulation -> Combine FASTA and QUAL" is the correct choice. You can do this before or after splitting. The assignment to "fastqsanger" can also be done before or after splitting. The issue you were most likely originally facing was leaving the data assigned as simply "fastq" (and possibly assigning fasta data as fastq).

This wiki has related help about datatypes and tools. I also added in a new line to cover this specific use case, should it help others:
http://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

I see that you have another question about genomes and GATK - I will respond to that thread separately.

Best,

Jen
Galaxy team
On 4/3/13 7:57 AM, Gema Sanz Santos wrote:
Hi Peter,

Thank you for your fast answer. 

I just want to know how can I use output files from Barcode splitter to use them into Bowtie for Illumina because I can´t see any tool to convert FASTA to FASTAQ. How can I continue with the mapping using the files from Barcode splitter? 

Best,
Gema

From: Peter Cock <p.j.a.cock@googlemail.com>
Date: Wednesday, April 3, 2013 4:42 PM
To: Gema Sanz Santos <ge2sasag@gmail.com>
Cc: <galaxy-user@lists.bx.psu.edu>
Subject: Re: [galaxy-user] Change format with "edit attributes"



On Wed, Apr 3, 2013 at 3:40 PM, Gema Sanz Santos <ge2sasag@gmail.com> wrote:
Hello,

I'm trying to change the format to the output files from Barcode splitter from FASTA to FASTAQ so I can use them in Bowtie for Illumina. I've read that it can be done through the edit attributes, I go to datatype and select fastaq, save and then go to convert format and press convert but the resulting file is 0 bytes and is not recognized by Bowtie. 

I´ve also tried to upload by copying the link and selecting fastaq as format but in this case, I got the file shown in the picture and it is not recognized by Bowtie again.


What can I do?? I don´t know how to continue because I´m not able to change the format to fastaq!

Thank you very much for your help in advance

Best,
Gema


Hi Gema,

There seem to be several factors confusing you here.

The screenshot shows FASTA data wrongly labelled as FASTQ.

The Galaxy "edit attributes" does NOT actually edit the data. There are separate tools which can convert from one format to another, which gives you a new entry in the history (another green box on the right).

You can convert from FASTQ to FASTA, but doing the opposite is not possible without inventing quality scores (e.g. give everything score 30).

Does that help?

Peter

 

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