Availability of the example datasets

[KarolienHeymans]

Hello,
I'm interested in following the tutorial, but the links to access the raw data are not working. Could you please let me know when the datasets will be made available? Thank you!

[gianmore]

Hi, same here. Thanks!

[danilexn]

Hi! Thanks so much for your messages! We have uploaded all data to GEO, and will be made available once the peer-reviewed publication is accepted. In the meantime, please let us know by email, and we can provide the raw data and/or processed h5ad files.

Let us know if this works for you 🤗

[KarolienHeymans]

Awesome! Thank you :)

[gianmore]

Thanks! Can you share to which email shall we contact you?

[gianmore]

Hi, Thank you. It will great if you could provide me both the raw and processed data for the mouse adult hippocampus so that I can follow along your tutorial. Thanks! Best, Gianluca

…

On Fri, 9 Feb 2024 at 10:44, Daniel León Periñán ***@***.***> wrote: Hi! Thanks so much for your messages! We have uploaded all data to GEO, and will be made available once the peer-reviewed publication is accepted. In the meantime, please let us know by email, and we can provide the raw data and/or processed h5ad files. Let us know if this works for you 🤗 — Reply to this email directly, view it on GitHub <#10 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFTOYSSLZCS4TTXXKBJFNJTYSXVZBAVCNFSM6AAAAABCZ5RWN6VHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4DIMJWHA3TO> . You are receiving this because you commented.Message ID: ***@***.***>

[danilexn]

@gianmore @KarolienHeymans see #16

[gianmore]

Thank you!!

[KarolienHeymans]

Thank you so much!

[KarolienHeymans]

Hello again! I couldn't locate an h5ad file name in the tutorial that corresponds to the one in the datasets. I'm curious to know at which stage this file was generated. Thank you!

[danilexn]

Hello! I will upload these h5ad files later today, sorry for the inconvenience!

[KarolienHeymans]

That would be very helpful, thank you.

[StevenSong]

would it be possible to share the fastq files from the barcode registration sequencing step?

[danilexn]

Hi @StevenSong!

We added links to download fastq files from the spatial barcode registration step - subsets of fc_1 and fc_2 that are relevant for the E13 and adult mouse samples. Enjoy 😉

https://rajewsky-lab.github.io/openst/latest/examples/datasets/

[StevenSong]

Perfect, thank you both

[gianmore]

Hi, I have maybe a stupid question.
During the configuration step of spacemake, when you add the specie, mouse in this case, which rRNA sequence have you used? --sequence <path_to_rRNA_sequences.fa>
Is it mandatory to have one?
Same for --sequence <path_to_phiX_genome.fa>

Thanks in advance!

[danilexn]

Hi!

It is not necessary, indeed.

With spacemake, you can specify mapping strategies (see map_strategy under "Sample parameters"). For mapping with genome only, you can specify a map_strategy like STAR:genome:final.

Hope this helps!

[gianmore]

it helps a lot, thanks! If I would like to use the rRNA also, from where could I download it? Thanks!