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Add content type for RNAseq (fq.gz) #5

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MaaikevS opened this issue Mar 2, 2022 · 7 comments · May be fixed by #74
Open

Add content type for RNAseq (fq.gz) #5

MaaikevS opened this issue Mar 2, 2022 · 7 comments · May be fixed by #74
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ContentType ContentType instances - addition of new or update of existing ones

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@MaaikevS
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MaaikevS commented Mar 2, 2022

The file type fg.gz is very common for RNA sequencing data and it would be great to add (especially since I have a dataset with many of these files)

@Majpuc
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Majpuc commented Mar 2, 2022

The extention .gz means that the files are compressed and can be found in principle on any other format that can be compressed. another example if the .tar compression. Is fq referring to FASTQ? fastq files are simple text files you don't need any special software to view them other then a text editor like notepad,wordpad.

@MaaikevS
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MaaikevS commented Mar 2, 2022

Thanks @Majpuc

fq indeed refers to FASTQ and it is indeed a compressed file. As far as I understand it will still need to be registered as its own content type because of the extension. Any thoughts @lzehl ?

@lzehl
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lzehl commented Mar 3, 2022

Not sure if I understand the issue correctly.

*.*.gz is not a separate content type if the respective software does not care if it is compressed version of the file or not.
For example, the content type for NIfTI-1 has both extensions: .nii and .nii.gz

How is the behavior for .fq and .fq.gz? Do we have already a content type for FASTQ ? Maybe .fq.gz is just missing from the extensions?

@Majpuc
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Majpuc commented Mar 3, 2022

I don't know for this particular extension. I just now that some sw would not open a compressed file directly and that the users will have to unzip the file before using it.

@MaaikevS
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MaaikevS commented Mar 3, 2022

We also do not have a FASTQ content type as far as I am aware.

@MaaikevS
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@lzehl Should we make a FASTQ content type here or not?

@lzehl
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lzehl commented Sep 9, 2022

@MaaikevS sorry that I did not respond in time.
Yes we should register at least register already the generic content type for the FASTQ file format.
NOTE: we need in addition the archive specific content types that seem to exist for FASTQ (cf. https://en.wikipedia.org/wiki/FASTQ_format and intro of http://maq.sourceforge.net/fastq.shtml)

@lzehl lzehl transferred this issue from openMetadataInitiative/openMINDS_core Nov 27, 2023
@UlrikeS91 UlrikeS91 linked a pull request May 7, 2024 that will close this issue
@UlrikeS91 UlrikeS91 self-assigned this May 7, 2024
@UlrikeS91 UlrikeS91 added the ContentType ContentType instances - addition of new or update of existing ones label May 8, 2024
@UlrikeS91 UlrikeS91 linked a pull request May 30, 2024 that will close this issue
@UlrikeS91 UlrikeS91 removed the PR made label Jun 4, 2024
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