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
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
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 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.
<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
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use 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:
To search Galaxy mailing lists use the unified search at:
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 dan@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 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.
<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
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use 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:
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use 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:
To search Galaxy mailing lists use the unified search at:
galaxy-user@lists.galaxyproject.org
-
Carlos Borroto -
Daniel Blankenberg -
Gema Sanz Santos -
Peter Cock