loading AS events

[rezarahman12]

Hi Maser team,

Thanks for developing this tool.

I've used rMATS turbo to identify differential splicing events. The results of rMATS are in the folder 'TTX-WT_versus_WT-ctr'. Please see my code below: getwd() [1] "C:/Users/uqmrah19/OneDrive - The University of Queensland/scaling project"

path [1] "~/scaling project/TTX-WT_versus_WT-ctr"

path <-("~/scaling project/TTX-WT_versus_WT-ctr/")

mydata <- maser(path, c("TTX", "CTR"), ftype = "JC") mydata A Maser object with 0 splicing events.

Samples description: Label=NA n= replicates Label=NA n= replicates

Splicing events: A3SS.......... 0 events A5SS.......... 0 events SE.......... 0 events RI.......... 0 events MXE.......... 0 events

I have a lot of significant AS events based on FDR<0.05, why it says 'A Maser object with 0 splicing events'?

Could you please help me on this issue? I desperately need to use maser.

Kind regards Reza PhD candidate The University of Queensland, Australia

[Oliverfeudj]

Hello @rezarahman12 Have you found a solution for this error, please? I am facing the same error for some of my output even though there are files from rmats run Thanks for your answer

[rezarahman12]

Hi @Oliverfeudj I've not received any feedback from the developer. So I abandoned using this package. Thanks

[Oliverfeudj]

Hi @rezarahman12 , I have found the solution for mine, check the directory that it is written correctly and that it contains rMATS output, also don't put a slash at the end of the directory when you create maser object, at least that's how I solved it. I hope it helps

[rezarahman12]

Thanks so much, @Oliverfeudj. I tried below, but unfortunately same. I appreciate it if you have suggestions. path <-("~/scaling project/TTX-WT_versus_WT-ctr")

the rMATS output in folder "TTX-WT_versus_WT-ctr"

mydata <- maser(path, c("TTX", "CTR"), ftype = "JC") mydata

mydata A Maser object with 0 splicing events.

Samples description: Label=NA n= replicates Label=NA n= replicates

Splicing events: A3SS.......... 0 events A5SS.......... 0 events SE.......... 0 events RI.......... 0 events MXE.......... 0 events

[Oliverfeudj]

@rezarahman12 send me your data, the output of rMATS in a zip file, I will have a look The error comes from the fact that it does not find anything in the directory you specified

[rezarahman12]

Thanks, Oliver (@Oliverfeudj).

Please find my rMATS output in this link: https://drive.google.com/drive/folders/15wMv-sifQl59zoI-zzFDMnL-gsDxlyyW?usp=sharing

Thanks for your consideration.

[Oliverfeudj]

@rezarahman12 I have added a folder to your shared drive with the script to upload the data. Let me know if you need another help

[rezarahman12]

Thanks Oliver. I ran the below but still no luck. ############################################################

Import files

#################################3########################## library(maser) AStypes_JCEC <- maser("./out", cond_labels=c("TTX", "CTR"), ftype ="JC") AStypes <- maser("./out", cond_labels=c("TTX", "CTR"), ftype ="JC") AStypes A Maser object with 0 splicing events.

Samples description: Label=NA n= replicates Label=NA n= replicates

Splicing events: A3SS.......... 0 events A5SS.......... 0 events SE.......... 0 events RI.......... 0 events MXE.......... 0 events

[Oliverfeudj]

@rezarahman12 set the working directory of R as the file location, this is a problem of directory.

Then do getwd() in R to see where it points

[rezarahman12]

Thanks a lot, Oliver! It worked now.

[Oliverfeudj]

Good!

[khdsudeep]

Hi, I am running with the same problem in loading rMATS output in maser. I saw that you both were able to solve the issue. Would you mind helping me out too.

Here is the code I ran:

library(maser) library(rtracklayer) path <- system.file("extdata", file.path("~/Desktop/rv1out"), package = "maser") test <- maser(path, c("shcon", "kd"), ftype = "JC") test

and this is what I got:

A Maser object with 0 splicing events.

Samples description: Label=NA n= replicates Label=NA n= replicates

Splicing events: A3SS.......... 0 events A5SS.......... 0 events SE.......... 0 events RI.......... 0 events MXE.......... 0 events

Thanks in advance!!!

-Sudeep

[Oliverfeudj]

Hello @khdsudeep Check your directory, that's where the error comes from. Maser is seeing your directory empty

Best

[khdsudeep]

Hey @Oliverfeudj, Thank you for help. I am able to load the file now.