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kharchenkolab / dropEst

Pipeline for initial analysis of droplet-based single-cell RNA-seq data
GNU General Public License v3.0
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RNA velocity using exon matrix as spliced and intron + spanning as unspliced #123

Open sarajimenez opened 3 years ago

sarajimenez commented 3 years ago

Hi,

I am trying to estimate the RNA velocities for a data set produced with the inDrops v2 sequencing protocol. For doing so, I'm starting with the fastq files downloaded from SRA. I've followed all the steps of the dropest pipeline as suggested here. However, I'm having some incompatibility problems in the step velocyto tools dropest_bc_correct. After, I've realized that I can directly use the output matrices of dropest as suggested in this issue #61. Therefore, I'm using the exon matrix as spliced transcripts, and the intron plus spanning matrix as unspliced transcripts. When estimating the RNA velocity I'm getting the following warning:

computing velocities WARNING: You seem to have very low signal in splicing dynamics. The correlation threshold has been reduced to -0.5209. Please be cautious when interpretating results.

Do you have any idea why I'm getting this? How to interpret it?

I'd highly appreciate any comment about it!

Best, Sara

ssanders0522 commented 8 months ago

Was this ever addressed? I'm having a similar issue