If you have any question about using DICEseq, you are welcome to discuss with the developer. Email: Yuanhua Huang <Y.Huang@ed.ac.uk>

Report bugs

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

Single time point

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.

Input sam files

Sorted and indexed sam file(s) are required for diceseq command. The format of sam_list is a string line, e.g.

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.

No output from DICEseq

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.


compatibility with pysam

If you are using pysam 0.8.2 or higher version, please use diceseq 0.1.2 or higher.

compatibility with numpy

If you are using numpy 1.8.2 or higher version, please use diceseq 0.1.3 or higher.