search

VCCRI / Sierra

Discover differential transcript usage from polyA-captured single cell RNA-seq data
GNU General Public License v3.0
49 stars 17 forks source link

Paired-end & PlotRelativeExpression functions. #62

Closed OnegItzhak closed 1 year ago

OnegItzhak commented 1 year ago

Hi.

First, thanks for the package. I found it very useful. I have a question and an issue:

Question: Does Sierra require paired-end data? If so, why?

Issue: When running one of the PlotRelativeExpression functions, I received an error. Upon checking, I found that these functions call the 'get_relative_expression_seurat' function, and in 'plotting_functions.R' line 124, an 'apply' function is used. The problem is that sometimes some of the clusters are shallow and do not have enough data, resulting in an empty vector that cannot be processed by the 'apply' function.

The solution I used was to subset the Seurat object and then run the PlotRelativeExpression functions. However, I believe that a better solution can easily be found by changing the function.

Best regards, Oneg Itzhak Halevi

rj-patrick commented 1 year ago

Hi @OnegItzhak, Thanks for the comment, I will look into the function. For your question, Sierra doesn't 'require' paired-end data per se. It was designed for barcoded UMI-based scRNA-seq technologies like 10x Chromium that utilise paired-end sequencing, but the insert itself is sequenced on one read. Cheers, Ralph