Idea: Supporting alevin output about tximport

[mikelove]

Thanks Pete,

This looks a good suggestion (haven't tried importing yet), and tximport probably makes sense as the place where it should live.

First thing I need to start working on it is some minimal example data that I can put into tximportData so we can have proper testing and vignette code. I'll coordinate with @rob-p and @k3yavi on it.

For timeline, I'm pretty busy the next few weeks with revisions and school starting, but we'll make it happen. Cool if we could do it before release in Oct.

[PeteHaitch]

I should have an alevin-processed dataset this week, but I don't think it'll be shareable. If @rob-p or @k3yavi already have one, that'd be ideal for inclusions in tximportData.

If you're interested in working together, I may have some time over the next few weeks to begin on this.

[k3yavi]

Hi guys,
Thanks for considering Alevin to be included in tximport, I think it would open up the gateway for Alevin to the awesome R world.
I have tried a stupid connection of Alevin -> R (Seurat) here although it starts from a csv file.
Not to bug @mikelove since I totally understand how busy it would be with the school opening up soon but when you guys have time the binary version of the matrix can be found here (inside folder alevin). Do let me know if you guys need any other help.

[mikelove]

@k3yavi what set of files should i put in tximportData to use for testing?

6.3K MappedUmi.txt
2.5K alevin.log
133K barcodeSoftMaps.txt
9.6M cell_eq_info.txt
2.4M cell_eq_mat.gz
5.0K cell_eq_order.txt
15K featureDump.txt
1.7K predictions.txt
1.6M quants_mat.gz
2.0M quants_mat_cols.txt
5.0K quants_mat_rows.txt
6.4K raw_cb_frequency.txt
5.9M transcripts.txt
1.6K whitelist.txt

[k3yavi]

Hi @mikelove ,

The relevant files would quants_mat* i.e.

• quants_mat.gz: the compressed matrix of double
• quants_mat_cols.txt: the name of the columns (gene names) in the above matrix.
• quants_mat_rows.txt: the name of the rows (CB) in the above matrix.

[mikelove]

Sorry this didn’t happen by release, got sidetracked by some revisions and other stuff. I’ll be working on this in the new development branch

[PeteHaitch]

Totally understandable, I've also not spent time on it either due to other commitments

[k3yavi]

No worries @mikelove .
Just let me know once you have a stable version, I'll just copy paste the R code to parse the quants here 😜 .

[k3yavi]

Hi @mikelove ,
There has been a couple of users asking for reading the gzip output format of Alevin in R, I am attaching a snippet of code which I wrote for parsing the output, hope it might help in tximport too. Please let me know if you see something that can be made more efficient in the attached R code.
readAlevin.R.txt

[mikelove]

In devel branch