trimmomatic input types (and phred64)

[bernt-matthias]

trimmomatic input types (and phred64)

[pjbriggs]

Hello @bernt-matthias

Apologies for not looking at this sooner.

1. It looks like Galaxy's fastqillumina type corresponds to Illumina 1.3+ format, which uses Phred64 quality encoding. It should be possible to add support for this format, if you can provide a small example file (an R1/R2 pair would be even better) with this format that I can use for testing (~10 reads should be sufficient).

2. I'm reluctant to add access for the -phred64 option directly. My feeling is that it's better to update the tool to support specific Galaxy-recognised FASTQ formats where the encoding is known, and have the tool add -phred64 when appropriate. Do you have a specific use case for this option?

Let me know what you think, best wishes

Peter

[bernt-matthias]

Thanks for coming back. Reporting is a long time ago and I cant recall the intended use case. I just read the documentation and found:

If no quality encoding is specified, it will be determined automatically (since version 0.32)

So I guess its best to leave it as it is and not support --phred33/--phred64 options, but rather just accept all fastq Galaxy data types and set the output type the same as the input type... ?

[pjbriggs]

Thanks for the clarification and additional information. I hadn't realised that Trimmomatic could determine the quality encoding automatically but as you say this would mean it's not necessary to implement explicit support for the -phred64 option.

As the tool already uses the format_source attribute to set the output type to match the input type (see the Galaxy tool documentation for info on this: https://docs.galaxyproject.org/en/release_18.05/dev/schema.html#id62), it does look like it's just a case of widening the acceptable input FASTQ types.

I'll need to generate some small FASTQs with different encodings for test cases (I guess "FASTQ Groomer" can do that for me). I'll update the thread once I've made some progress.

[bernt-matthias]

Great. Good idea to use FASTQ Groomer.

[pjbriggs]

Now in tool version 0.36.6 & uploaded to toolsheds, so closing this as done.