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rstickels / Slide_seqv2

notebooks for loading Slide-seqV2 data and some associated analyses
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Getting spliced and unspliced counts #2

Open pekjoonwu opened 2 years ago

pekjoonwu commented 2 years ago

Hey,

Thanks for develpoing this good method and also very high quality data! I am wondering what kind of tools did you guys use to get spliced and unspliced counts and does it matter if the tools are developed for single cell datasets?

Thanks!

qiaochen commented 2 years ago

Thanks for opening the issue and, of course, the authors of this Github repository. I am trying to replicate the RNA velocity estimation in Fig3. of the SlideSeq2 Paper, but had some problem processing the bam file Puck_190921_19.bam (accessible through URL. I noticed the cell barcodes in the bam file has 15 characters, but those in the annotation/spaital files (i.e., Puck_190921_19.digital_expression.txt.gz/Puck_190921_19_bead_locations.csv) have 14-character barcodes.

So, is one character trimmed? If so, would you please indicate the trimmed position? I am trying to count Spliced and Unspliced counts using velocyto or dropEst, both requiring a barcode file for input, for which I got stuck.

Thanks!