If you have any question about using DICEseq, you are welcome to discuss with the developer. Email: Yuanhua Huang <Y.Huang@ed.ac.uk>
If you find any error or suspicious bug, I will appreciate your report. Please write them in the github issues: https://github.com/huangyh09/diceseq/issues
Though DICEseq is developed for time series RNA-seq, it also performs very well
for single time point, like most RNA-seq experiment. With theta1=3.0, you
should get similar results as MISO.
Sorted and indexed sam file(s) are required for diceseq command. The format
of sam_list is a string line, e.g.
sam_list=$sam_dir/sam1_rep1.sorted.bam,$sam_dir/sam1_rep2.sorted.bam---$sam_dir/sam2.sorted.bam---$sam_dir/sam3.sorted.bam
diceseq --anno_file=$anno_file --sam_list=$sam_list --out_file=$out_file
Please do not directly use a list file containing the sam files. Otherwise you
need load it via bash command by yourself. Note: the delimiter , means
merging the two samples, and --- means different time points.
Currently, DICEseq requires gtf/gff3 file with specific order. gene–>transcript1–>exon1...exon_k–>transcript2...
If the annotation is not in such sorted or if there is no isoform annotation, you probably won’t get any output.