visualize sashimi plot with brie2

[TuoCai2000]

Hello!Thank you for developing Brie! Recently I tried to visualize sashimi plot with Brie2's h5ad files. However,I noticed that I had to use Brie1's results(samples.csv.gz)to draw the sashimi plot with miso's sashimi_plot command. Samples.csv.gz includes the MCMC samples of posterior distribution of Psi,however,h5ad files don't contain this information given that Brie2 doesn't use Metropolis-Hastings algorithm to approximate the posterior. So I would like to verify if sashimi plot can only be generated with Brie1's result? Thank you so much!

[yiyisun682]

Hello!Thank you for developing Brie! Following up on the previous question raised by TuoCai2000, I would like to ask if there is a script that can directly use the .h5ad file generated by Brie2 to draw the sashimiplot?

[huangyh09]

Thanks @TuoCai2000 and @yiyisun682 for being interested in the sashimi function. Unfortunately, it's indeed only available for brie1's results and doesn't support h5ad file.

Potentially, you can extract the specific cell types into sub-bam file(s) and make sashimi plots by treating them as bulk samples: https://github.com/huangyh09/briekit/tree/master/sashimi_plot Note, this only supports Python 2 (which you can create with conda environment).

For extracting cells from a bam file with samtools view:

samtools view -D BC:barcodes.txt -o /data_folder/data.barcodes.bam /data_folder/data.bam

Yuanhua

[yiyisun682]

Thank you very much for your answer and we will make further attempts according to your suggestions.