How to format fastq data for tools that require .fastqsanger format?

• Most tools that accept FASTQ data expect it to be in a specific FASTQ version: .fastqsanger. The .fastqsanger datatype must be assigned to each FASTQ dataset.

In order to do that:

• Watch the FASTQ Prep Illumina video for a complete walk-through.
• Run FastQC first to assess the type.
  • Run FASTQ Groomer if the data needs to have the quality scores rescaled.
  • If you are certain that the quality scores are already scaled to Sanger Phred+33 (the result of an Illumina 1.8+ pipeline), the datatype .fastqsanger can be directly assigned. Click on the pencil icon galaxy-pencil to reach the Edit Attributes form. In the center panel, click on the “Datatype” tab, enter the datatype .fastqsanger, and save.
• Run FastQC again on the entire dataset if any changes were made to the quality scores for QA.

Other tips

• If you are not sure what type of FASTQ data you have (maybe it is not Illumina?), see the help directly on the FASTQ Groomer tool for information about types.
  • For Illumina, first run FastQC on a sample of your data (how to read the full report). The output report will note the quality score type interpreted by the tool. If not .fastqsanger, run FASTQ Groomer on the entire dataset. If .fastqsanger, just assign the datatype.
  • For SOLiD, run NGS: Fastq manipulation → AB-SOLID DATA → Convert, to create a .fastqcssanger dataset. If you have uploaded a color space fastq sequence with quality scores already scaled to Sanger Phred+33 (.fastqcssanger), first confirm by running FastQC on a sample of the data. Then if you want to double-encode the color space into psuedo-nucleotide space (required by certain tools), see the instructions on the tool form Fastq Manipulation for the conversion.
  • If your data is FASTA, but you want to use tools that require FASTQ input, then using the tool NGS: QC and manipulation → Combine FASTA and QUAL. This tool will create “placeholder” quality scores that fit your data. On the output, click on the pencil icon galaxy-pencil to reach the Edit Attributes form. In the center panel, click on the “Datatype” tab, enter the datatype .fastqsanger, and save.

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