about output of diceseq

[xflicsu]

Hello Huang,

I use diceseq to count reads from RNA-seq data with total library.
But, I do not understand the mean of output file (xx.dice).
Could you show me the mean of every column?

BWT, if I use parameter of "--add_premRNA", could it work for poly(A) captured mRNA-seq?

diceseq -a $anno_file -s $sam_file -t 1,5 --add_premRNA=True -o xx

gene_id transcripts count_T1.0 ratio_T1.0 95CI_T1.0 count_T5.0 ratio_T5.0
95CI_T5.0
YDL219W YDL219W,YDL219W.p 76 0.348 0.132:0.557 74 0.589 0.383:0.777
YDL191W YDL191W,YDL191W.p 136 0.553 0.410:0.680 116 0.807 0.722:0.870
YDL136W YDL136W,YDL136W.p 129 0.553 0.350:0.698 123 0.763 0.644:0.851
YDL130W YDL130W,YDL130W.p 78 0.312 0.164:0.460 64 0.480 0.322:0.646

[huangyh09]

Hi Xianfeng,

Thanks for using DICEseq and share your experience.

First of all, for reads count, you should run "dice-count" rather than "diceseq". Then you will have different results, like:
https://github.com/huangyh09/diceseq/blob/master/data/out/t3_cnt1.txt
https://github.com/huangyh09/diceseq/blob/master/data/out/t3_cnt2.txt

You could also have a look of the updated manual, which contains some demo: http://diceseq.readthedocs.org/en/latest/

Regarding to the "--add_premRNA", it is only for adding the pre-mRNA as an isoform when quantifying the proportion of mature mRNA from the library containing pre-mRNA too.

In any case, it should work for poly(A) captured mRNA-seq.

Any question is welcome, and the FAQ will be updated accordingly.

Best wishes,
Yuanhua