mapping quality scRNA seq

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4.5 years ago

annaA ▴ 10

Hey everyone,

I am working with single-cell RNA seq data and now I want to check the mapping quality. I've read about couple of tools I can use, like fastqc,RSeQC etc My question is which is better and how I choose if I need to filter out some reads?

Thanks in advance
Anna

mapping single-cell-RNA RNA-Seq • 924 views

ADD COMMENT • link updated 17 months ago by Ram 44k • written 4.5 years ago by annaA ▴ 10

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What program are you using for analyzing your scRNAseq data? e.g. if you have 10x data you may want to use the statistics produced by cellranger.

ADD REPLY • link 4.5 years ago by GenoMax 147k

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My plan is to use Seurat

ADD REPLY • link 4.5 years ago by annaA ▴ 10

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Sure but seurat is for secondary analysis. What are you using for alignment of the data?

ADD REPLY • link 4.5 years ago by GenoMax 147k

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oh ok. Hisat2 with argument -k 1

ADD REPLY • link 4.5 years ago by annaA ▴ 10

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