=== FAQ === Contacts ======== If you have any question about using DICEseq, you are welcome to discuss with the developer. Email: Yuanhua Huang 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. :: 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. 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. Compatibilities =============== 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.