brie

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filter out low coverage event

1

Hi, Yuanhua, I'm using BRIE to calculate Psi for each event, and then perform different AS detection with △Psi>0.05 and P

jphe

Dearest Yuanhua, Running brie with a specific bam file generates this error. Other bam files that I have tried work perfectly fine. ``` Traceback (most recent call last): File "/home/user/anaconda3/envs/brie-env/bin/brie",...

trevortknguyen

Other spling types filter (A5SS, A3SS, MXE, RI)

2

Hi, I did not see any examples analyzing other splicing types (A5SS, A3SS, MXE, RI) using BRIE. I used brie-event-filter to deal with gff3 of other splicing types, but I...

chenjiwei124128

brie-event cannot read .gtf file

6

Hi, I am trying to use BRIE using a custom annotation file and the GENCODE M10 annotation file. In both cases, running `brie-event` as follows: `brie-event -a gencode.vM10.annotation.gtf` returns errors...

aarzalluz

Counts in fractions.tsv

2

Dear Yuanhua, This is more a question than an issue. I recognized that the counts in the fractions.tsv file can adopt non integer values, because the counts are the mean...

linkerst

brie-count smartseq3 bam

1

Hello, I would like to ask how to analyze smartseq3 data in brie2, and how to set --UMItag in brie-count to obtain umi reads and internal reads at the same...

lishuangshuang0616