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 <[email protected]
<mailto:[email protected]>>
Date: Wednesday, April 3, 2013 4:42 PM
To: Gema Sanz Santos <[email protected] <mailto:[email protected]>>
Cc: <[email protected] <mailto:[email protected]>>
Subject: Re: [galaxy-user] Change format with "edit attributes"
On Wed, Apr 3, 2013 at 3:40 PM, Gema Sanz Santos <[email protected]
<mailto:[email protected]>> 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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