supported species

[pengxin2019]

Hi there, I noticed you mentioned in one of the previous question that a tutorial for non-human and non-mouse species could be provided. Is that tutorial available now?

Thanks for developing this tool.

Best Pengxin

[pengxin2019]

Also, do you think that the inference of transcriptional regulators using LISA(scRNA) and GIGGLE(scATAC) would work for non-human non-mouse species? I feel like it would probably not since the datasets(CistromeDB and GIGGLE) are the chip-seq profiles of human, right?

Is my understanding correct?

Thanks Best Penny

[crazyhottommy]

We have not done anything to support other species. Yes, the LISA will only work for human and mouse data. We will consider supporting other species if there is a strong desire from the community.

[baigal628]

Also, do you think that the inference of transcriptional regulators using LISA(scRNA) and GIGGLE(scATAC) would work for non-human non-mouse species? I feel like it would probably not since the datasets(CistromeDB and GIGGLE) are the chip-seq profiles of human, right?

Is my understanding correct?

Thanks Best Penny

Hi Penny,

Which specific species do you want MAESTRO to support? I can try to write down a tutorial for species other than human and mouse.

Thanks, Gali

[pengxin2019]

Hi Gali, The species that I am interested in is pig (Sus scrofa). Thanks for providing the offer to write down the tutorial specially for pigs. It would be helpful to us.

But like what I mentioned in my last email, I am also worried about the inference of transcriptional regulators for pigs using LISA(scRNA) and GIGGLE(scATAC). Would that work? Datasets(CistromeDB and GIGGLE) are the chip-seq profiles of humans, right?

Thanks Best Penny

On Mon, Jun 28, 2021 at 3:06 PM Baigal @.***> wrote:

Also, do you think that the inference of transcriptional regulators using LISA(scRNA) and GIGGLE(scATAC) would work for non-human non-mouse species? I feel like it would probably not since the datasets(CistromeDB and GIGGLE) are the chip-seq profiles of human, right?

Is my understanding correct?

Thanks Best Penny

Hi Penny,

Which specific species do you want MAESTRO to support? I can try to write down a tutorial for species other than human and mouse.

Thanks, Gali

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/liulab-dfci/MAESTRO/issues/140#issuecomment-869997957, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANC7BUQQAUCPDTQ4DMKVWWDTVDI5BANCNFSM47CQV5WQ .

[baigal628]

Hi Penny,

Yes. Current LISA and GIGGLE only have data references for human and mouse.

Best, Gali

[pengxin2019]

Dear development team of MAESTRO,

Good morning. I hope you are doing well.

Last time you mentioned that a tutorial for pig is not available yet and you can generate such a tutorial for pig if we are interested in that. Just want to follow up with the tutorial for pig (Sus scrofa). Have you started composing this tutorial? If not, I want to confirm my interest in it. Just in case you need it, relatively speaking, we prefer getting the annotation file or preference genome from ensembl ( https://useast.ensembl.org/index.html?mobileredirect=no) rather UCSC.

By the way, is the fastq file the only acceptable input file for MAESTRO? Not sure which exact steps are specific to pigs. Maybe I can start even before the pig tutorial is ready if it accepts other formats of input?

Thanks Best Penny

Pengxin (Penny) Yang

Ph.D. Student

office: 2258 Kildee Hall

@.***

Iowa State University

On Tue, Jun 29, 2021 at 7:53 AM Baigal @.***> wrote:

Hi Penny,

Yes. Current LISA and GIGGLE only have data references for human and mouse.

Best, Gali

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[crazyhottommy]

@baigal628 can you please ask @pengxin2019 for a list of genome annotation files so we can expose MAESTRO to accept them? we can then write a tutorial for other species. Thanks!

[baigal628]

Hi @pengxin2019,

I am going to work on a tutorial for supporting other species in MAESTRO. To do that, I need several genome annotation files from pig for illustration. Could you please help to provide a list of the below files at your convenience? Also, if you have the link for a pig single-cell test data, it would be better for me to test on that.

Thanks!

scRNA-seq: reference.fa (for STARsolo) RefSeq.bed (Optional: for rseqc reads distribution) HouseKeepingGenes.bed (Optional: for rseqc gene coverage)

scATAC-seq: reference.fa (for minimap2/Chromap) promoter.bed (for QC fraction of reads in promoter) chrom_len.txt (Obtained by UCSC fetchChromSizes, for generating bigwig file) ensemble.bed (gene annotation file)

[crazyhottommy]

@pengxin2019 we are much interested in supporting other species, if you can provide some example data that would be great. thx.

[htong3031]

@crazyhottommy @baigal628 Hi, I‘m currently encountering a similar situation that I want to use the tool in Arabidopsis. What should I do to calculate gene score according to scATAC peak count for a species other than human and mouse? If any tutorial supporting other species available yet? Thank you.