Minghao

how does whippet define exon skip events?

5

can Whippet detect exon skip events? it seems that CE (core exon) doesn't contain exon skip. Thank you!

error occurred when running JUM_B.sh

1

Hi, I got errors when running JUM_B.sh what I ran: ```shell cd ~/projects/AS/analysis/paper_gb/ sim_1//JUM/JUM_diff/ && bash ~/bin/JUM-JUMv2.0.2_short_user_argument_BSD//JUM_B.sh --Folder ~/bin/JUM-JUMv2.0.2_short _user_argument_BSD/ --Test adjusted_pvalue --Cutoff 0.05 --TotalFileNum 8 --Condition1_fileNum_threshold 3 --Conditio n2_fileNum_threshold...

thread 'main' panicked at 'McFly error occurs each time I run some command.

2

Hi! Thank you for developing this incredible tool. I got this following error each time I run a command in the terminal. I have `export TMPDIR=~/tmp/` in my `.zshrc`. How...

Discrepancies between sniffle 2.0.7 and sniffle 2.2

3

Hi! I have a patient sample with a known gene fusion/genomic translocation (i.e. PAX5::ETV6). Sniffle 2.0.7 did call this BND in the vcf by running `sniffles --input mysample.bam --vcf out.vcf...

what I did: ``` simulate_experiment_countmat(fasta = "~/doc/reference/fa/gencode.v32.transcripts.fa", readmat = merges, outdir = "~/tmp/polyester/") ``` the error: ``` Error in h(simpleError(msg, call)) : error in evaluating the argument 'i' in selecting...

how can I get annotated events?

1

hello, Thank you for your detailed codes. However I got a question. I'd like to know if I can directly get which alternative splicing event is annotated in the gtf...