muhligs / mireact

Estimate microRNA activity in single cells

miReact

Software to estimate miRNA activity from mRNA expression in single cell data.

Read about it here (Scientific Reports)

Or here (BioRxiv version)

mireact's Issues

Further information about patterns.7mer.Rdata

Hi,
Thanks for developing this method and sharing the code. I'd like to try this approach, however I'd like to understand a bit further about the processing of the motifs. I see that miReact analysis is based on having an existing patterns list which is loaded from the file patterns.7mer.Rdata. Would it be possible to share how this list was generated? Also, is there any documentation of the "pattern" object which is stored in the patterns list?
Many thanks,
Karen

Issue in running miReact

Hi!

First of all thank you for this tool! I am not an expert but I would like to use it on my data (skin human keratynocites) and I am not able to do it...

I downloaded the motif probability files from Synapse and I put them in the motif.models folder
Then I prepared my own expression data set (13307 genes, 1614 cells) and I put it in the data folder

So I used these commands to generate the output file:

- source ("~/miReact/code/mireact.R")
- efile <- "~/miReact/data/MeP_mireact_exp.rds"
- mireact(exp=efile, species="hs", motifs=7, seq.type="utr3", out.file= "~/miReact/data/mirnaActivity_MeP_K82.rds", out.meonly=T, install.dir = "~/miReact")

After running them, I have this message on RStudio:

creating directory: /home/grazia/miReact/o2022-06-2212:20:09
[1] "Follow progress in /home/grazia/miReact/o2022-06-2212:20:09/Rscript-[jobid].out"

So no error in R but the whole process fails because I obtain only a new folder with 3 files

- e.RData (I obtain this error when I try to open it:
  Error: bad restore file magic  number (file may be corrupted) -- no data loaded)
- runparameters.RData
- sbatch.script

and no Rscript-[processID].out or my output file in the data folder.

Do you have any suggestion?

Thank you and have a good day!

miReact for Drosophila

Awesome tool.

Is there a tutorial that I can obtain the 3'UTR sequences for Drosophila? Thanks!

3' UTR seqlist

Maybe I'm missing something, but if I understand your tutorial correctly, I need to input the 3' UTR seqlist from my own experiment, is that correct? In that case, could you describe how I obtain this from, e.g., 10X experiments (FASTQ or BAM)?
Thanks!

miReact running on a local computer problem

Hello. I am interested in analysing human datasets, so I was having a go with the ones located in miReact. I tried running the code on a 32GB machine but when I use the mireact() function I get this error: “sbatch is needed”. This isn’t being run on a cluster, so I wonder if there is a option in the function for not going through sbatch but running directly on the computer or a ‘NULL’ option? We aren’t worried about long runtimes.
Thank you very much in advance!

Running for other species

Hi! I am using miReact in non-mouse or human species. I experience problems in running, already fixed (I guess). I am a python user so I am not entirely sure, but, said that:

First

When running miReact it stops in addMotifs.R:
line 25 pval.mat <- pval.mat[,sco$seqs$tid]

I "fixed" it by adding to the tutorial code (miReact_tutorial.pdf) the followings lines:
which generates the missing colnames in the sp.seqXmot.utr3_mrs_7mer.rds file. Sames as sp.seqXmot.counts.utr3_mrs_7mer.rds colnames.
The program runs and gives me the output file, but, Is this change correct?

dim(pval.mat)
############
#added lines
seqs <- readRDS("./seqs/sp.utr3.seqs.rds")
colnames(pval.mat) <- seqs$tid
############
saveRDS(pval.mat, file="./motif.models/sp.seqXmot.utr3_mrs_7mer.rds")

Second

Also, looking inside addMotifs.R code I find what I guess are typos in the variable moitfs in lines:

line 14 if(file.exists(file)) load(file) else stop(paste0("Please prepare motif models for ",moitfs,"-mers."))
line 21 if(!file.exists(file)) stop(paste0("Please prepare sequence specific probabilities for ",moitfs,"-mers in species ",sco$runparameters$species,"."))
line 33 if(!file.exists(file)) stop(paste0("Please prepare motif counts for ",moitfs,"-mers in species ",sco$runparameters$species,"."))

Third

My expression df uses gid instead of tid, I get the output files, so, this is not a problem, right?
I interpret that miReact handles it based on this message:
#Chosen identifier: Ensembl gene ID .

Thanks you very much in advance!