Hi Gema,

Quick comment. If you do have the QUAL file to begin with, I would
recommend doing the combine first, then barcode splitter(which can do
fastq too), then bowtie. This way you have the benefits of mapping
using the real quality score.

--Carlos


On Wed, Apr 3, 2013 at 11:07 AM, Daniel Blankenberg <d...@bx.psu.edu> wrote:
> Hi Gema,
>
> For example, see the "Combine FASTA and QUAL into FASTQ" tool for creating a
> FASTQ file from FASTA data; when quality data is not provided, fake score
> values will be used.
>
>
> Thanks for using Galaxy,
>
> Dan
>
> On Apr 3, 2013, at 10:42 AM, Peter Cock wrote:
>
>
>
> On Wed, Apr 3, 2013 at 3:40 PM, Gema Sanz Santos <ge2sa...@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.
>>
>> <Screen Shot 2013-04-03 at 4.37.50 PM.png>
>>
>> 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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___________________________________________________________
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