Add AnnData output process about scrnaseq HOT 18 CLOSED

Hi Guys. Just to let you know that I am working on adding a module for that, which is also mentioned in issue #89
😄

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Thought scverse IO package when you mentioned was the whole scverse of functions 😅

But they are actually planning to have everything as a single package? Is that so?

Anyways, so we have a plan!
Monday I come back with my saga to find a docker image. The module itself is finished with scanpy 😃

Have a nice weekend guys

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Yes, the module I am writing is using scanpy from scverse IO package to handle convertion.

Well, the scverse IO package doesn't exist yet which is a common complaint :) You have to use scanpy as you were planning to do anyways.

"What do you guys think?"
Good plan!

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"But they are actually planning to have everything as a single package? Is that so?"

"they" are the people you're talking to here :) Yes, this has been a frequent discussion.

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Yeah because I think that the actual count generation is not done in the pipeline (yet). Could be added, I think this is just lacking some extra parameters / another step that generates the matrices that @ivirshup just mentioned above.

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Available in dev now!

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Sounds like a good thing to do - maybe work on this already in DSLv2 as the conversion to DSLv2 is likely going to be finalized during the hackathon ...?

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@fmalmeida it might make sense to make the module more general -> create scverse datastructures.
Especially with #99 the output should be MuData objects and not AnnData objects. Happy to get more detailed if you want me to.

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Would be great to align here @fmalmeida with @Zethson 👍🏻

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Of course Lukas is right - but wouldn't it be a good start to add AnnData support and extend to mudata whenever we address #99?

I guess it depends if that feature is planned for the 2.1 release...

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@grst I also think that this is another great use case for the scverse IO package @ivirshup
The containers get a bit bloated with the big packages.

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Hi @grst, @apeltzer and @Zethson.

Yes, the module I am writing is using scanpy from scverse IO package to handle convertion. It is basically done. I just need to find a working docker image for it (It is not in bioconda — helps on that are welcomed)

I believe we can do as Greg mentioned because they are different use cases.

I also saw that there is an issue #89 about converting to Seurat format (which I will also work on).

Since they are all diferente and valid use cases, I believe all of them should be options.

We can have modules for AnnData, Seurat and MuData. And later, if necessary, make then optional for users.

We could, for example, do:

1. First have AnnData
2. Have Seurat
3. Work on #99 and then add MuData.

What do you guys think?

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Didn’t know.
Great work on the packages 😁

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Hi Guys,
A question.

How can I do conversion for other aligners? For now I was able to do for cellranger, alevin and kallistobustools with scanpy.read_10x_mtx and scanpy.read_mtx but am not sure about starsolo. It that does not seem to produce .mtx file.

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I have opened a draft PR so we can try to address stuffs like right concept, right usage of data and storage of outputs directly from there.

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AFAICT, start solo should output something like that? From the bottom of the docs:

soloOutFileNames            Solo.out/          features.tsv barcodes.tsv        matrix.mtx
    string(s)               file names for STARsolo output:
                            file_name_prefix   gene_names   barcode_sequences   cell_feature_count_matrix

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Interesting ...
This is not what I am seeing.

run_star
└── star
    ├── Sample_X.Aligned.sortedByCoord.out.bam
    ├── Sample_X.Log.final.out
    ├── Sample_X.Log.out
    ├── Sample_X.Log.progress.out
    ├── Sample_X.SJ.out.tab
    ├── Sample_Y.Aligned.sortedByCoord.out.bam
    ├── Sample_Y.Log.final.out
    ├── Sample_Y.Log.out
    ├── Sample_Y.Log.progress.out
    ├── Sample_Y.SJ.out.tab
    └── star
        ├── Genome
        ├── Log.out
        ├── SA
        ├── SAindex
        ├── chrLength.txt
        ├── chrName.txt
        ├── chrNameLength.txt
        ├── chrStart.txt
        ├── exonGeTrInfo.tab
        ├── exonInfo.tab
        ├── geneInfo.tab
        ├── genomeParameters.txt
        ├── sjdbInfo.txt
        ├── sjdbList.fromGTF.out.tab
        ├── sjdbList.out.tab
        └── transcriptInfo.tab

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