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liulab-dfci / MAESTRO

Single-cell Transcriptome and Regulome Analysis Pipeline
GNU General Public License v3.0
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supported species #140

Open pengxin2019 opened 3 years ago

pengxin2019 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

Hi Penny,

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

Best, Gali

pengxin2019 commented 3 years ago

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

— 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-870573307, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANC7BUWEMLQFHYTPWJMTB7DTVG653ANCNFSM47CQV5WQ .

crazyhottommy commented 3 years ago

@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 commented 3 years ago

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 commented 3 years ago

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

htong3031 commented 1 year ago

@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.