Minimap2 accepted formats

usegalaxy.eu support
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1

Hi there, this is a minor issue, but in Minimap2, the accepted formats are:

  • fastqsanger

  • fastqsanger.gz

  • fasta

But other options, like ‘fastq’ or ‘fastq.gz’ should be accepted as well.

Hope this could help.

Best, Agustin.

2

Hi @Agustin_Baricalla

This is a good question. Tools that are sensitive to quality score scaling will often expect that the scaling used is declared. This is a type of metadata encoded in the datatype.

The fastqsanger/gz datatype variations describe the Sanger Fastq +33 offset scaling.

This is produced from Illumina 1.8+ sequencing protocols but is also used for many Single Cell protocols (whether actual or with some default value).

When loading data through the Upload tool, it is usually a good idea to use all default settings. This allows Galaxy to auto-detect the datatype. For read data, a quick sanity check confirming the quality score scaling is run on the loaded read files followed by assigning the appropriate datatype metadata.

All data is checked this way. An unexpected result is informative. There might be a data issue to correct or more may be going on. For reads, transforming between scaling schemes is possible! Please ask if this is your use case. Or see the FAQs here for some known cases/solutions.

What to do

If the datasets are already in your history, you can update the metadata directly or auto-detect it again.

Please let us know if this helps or not! If not, would you be able to share what kind of reads you have? Where were they sourced may matter too. Let’s start there, thanks! :slight_smile: