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Question: Change Format With "Edit Attributes"
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gravatar for Gema Sanz Santos
5.7 years ago by
Gema Sanz Santos • 110
European Union
Gema Sanz Santos • 110 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
alignment bowtie • 1.2k views
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modified 5.7 years ago by Peter Cock • 1.4k • written 5.7 years ago by Gema Sanz Santos • 110
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gravatar for Peter Cock
5.7 years ago by
Peter Cock • 1.4k
European Union
Peter Cock • 1.4k wrote:
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
ADD COMMENT • link written 5.7 years ago by Peter Cock • 1.4k
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
ADD REPLY • link written 5.7 years ago by Daniel Blankenberg ♦♦ 1.7k
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
ADD REPLY • link written 5.7 years ago by Carlos Borroto • 390
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