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PacificBiosciences / pbbioconda

PacBio Secondary Analysis Tools on Bioconda. Contains list of PacBio packages available via conda.
BSD 3-Clause Clear License
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isoseq for scRNA: UMI with homopolymers are not removed #692

Closed JiangyanYu closed 1 month ago

JiangyanYu commented 2 months ago

Operating system Linux

Package name smrtlinks v13

Conda environment not used in installation

Describe the bug UMI AAAAAAAAAAAA are found in the annotated.info.csv.

Error message not a program error.

To Reproduce grep AAAAAAAAAAAA in annotated.info.csv

Expected behavior In the 10x cellranger pipeline, molecules with homopolymers UMI are removed, might be due to low quality. Can you please explain further why these molecules are included in the isoseq pipeline? Thanks very much!

armintoepfer commented 1 month ago

You need to remove them on their own.