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YiPeng-Gao / scDaPars

Dynamic Analysis of Alternative Polyadenylation from single-cell RNA-seq (scDaPars)
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pipeline #5

Closed ghost closed 3 years ago

ghost commented 3 years ago

Is the flow chart missing 3 steps and not displayed?

  1. selected reads with correct unique molecular identifier (UMI) using Drop-seq tools FilterBAM (Macosko et al. 2015)
  2. remove reads with duplicated UMIs using UMI-tools dedup (Smith et al. 2017).
  3. merged reads originated from same cells together and generated one BAM file for each single cell

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YiPeng-Gao commented 3 years ago

Is the flow chart missing 3 steps and not displayed?

  1. selected reads with correct unique molecular identifier (UMI) using Drop-seq tools FilterBAM (Macosko et al. 2015)
  2. remove reads with duplicated UMIs using UMI-tools dedup (Smith et al. 2017).
  3. merged reads originated from same cells together and generated one BAM file for each single cell

image

image

This is standard procedure for any 10X (UMI-based protocol) single cell procedure, not specific to scDaPars that is why it is not included in the pipeline.