Comments (2)
Dear Stephanie,
Thanks for the good question, and checking the codes. As inputs, the counts for a whole splicing event are integer values, however, when assigning these reads to either exon-inclusion isoform or exon-exclusion isoform, it takes the posterior probability, which is a float. That is why you see them as non integer values. When you add up the counts for the two isoform, i.e., xx.in and xx.out, it will be very close to an integer. For simplicity, you could take the float value as an integer with round()
function, which may sacrifice some precision, and is taken for the output file of differential splicing by brie-diff
.
In the script, the Cnt_all
is the counts supporting each isoform for all splicing events. This is based on the estimate of the fractions of each isoform (within a gene), i.e. Psi, and then multiply to the total counts of that gene, with weights of isoform length.
So, the counts are very informative, and is good for using as threshold when selecting genes for analysis, though the confidence interval is also a good option.
I will add more details on the output counts into the manual.
Cheers,
Yuanhua
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Hi Yuanhua,
Has the manual been updated yet with more information about how the count values mentioned in the first section of the manual are calculated? I'm interested in understanding the tool better, as I'm considering using it for my own analyses, but quantification methods are crucial, and I cannot find details about them anywhere in the documentation.
Cheers,
Ángeles
from brie.
Related Issues (20)
- Brie-Count and Brie-Quant Errors HOT 7
- Other AS types counting, no output HOT 6
- the output of brie-count has not .h5ad file HOT 1
- the output of brie-count don't contain the .h5ad file HOT 3
- the errors about the brie-count HOT 2
- brie-quant uses all available resources HOT 1
- visualize sashimi plot with brie2 HOT 3
- multiple 10x samples integration to run brie-count HOT 1
- Brie-count Multiprocessing using only 1 core HOT 2
- some questions about psi distribution
- Brie-count error with paired end smart-seq2 data HOT 1
- confused about Psi_95CI HOT 1
- p values outputfile
- MXE chromosomecoordinates to gene_ids
- How to get the specific sites where differential splicing events occurs
- ELBO_gain and effect size HOT 1
- split cells into groups and run brie2 HOT 3
- Error when running brie-count: IndexError: list index out of range HOT 1
- UnicodeDecodeError HOT 1
- Is BRIE2 appliable in 10x Genomics scRNA data HOT 4
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