Regarding DICAST command

[PRIYANKA-22091995]

Hello Team,

I have a basic query regarding the fastq reads , i don't have fastq reads in pairs, i have single fastq reads generated from direct rna sequencing(SQK-RNA002), is it possible to run DICAST for detection of alternative splicing events.It would be nice to have your insights on the same.

Thanks&Regards
Priyanka Roy

[amitfenn]

Hi Priyanka,
All tools, by default try alignment for pairs reads. But if the files are not named as "*1.fastq" or "*2.fastq", this leads to an error which automatically triggers single read alignments. This means, all mapping tools would be technically able to handle single reads by default.

Also, since you do not need ASimulatoR, nor the entire repertoire of tools within DICAST, you could simplify the pipeline by running each tool on it's own.

For ONT reads, I'd recommend minimap from our repertoire as an aligner. Please read the compatibility table here. For splicing tools this means that after minimap, you have only the following splicing tools available to you: irfinder; majiq; spladder; whippet.

I should also recommend running minimap by yourself with your favorite flags, because you have a platform specific case (DICAST is optimised for illumina reads). As long as you maintain this directory structure, running the other tools with the default command (docker run -v **<your mounted folder>**:/MOUNT --user $(id -u):$(id -g) dicastproj/dicast:irfinder), for each (irfinder; majiq; spladder; whippet) on it's own should yield you the best results the fastest.

Best of luck :)
Amit.