mapping quality scRNA seq

0

Entering edit mode

4.6 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 • 928 views

ADD COMMENT • link updated 17 months ago by Ram 44k • written 4.6 years ago by annaA ▴ 10

0

Entering edit mode

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 4.6 years ago by GenoMax 147k

0

Entering edit mode

My plan is to use Seurat

ADD REPLY • link 4.6 years ago by annaA ▴ 10

0

Entering edit mode

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

ADD REPLY • link 4.6 years ago by GenoMax 147k

0

Entering edit mode

oh ok. Hisat2 with argument -k 1

ADD REPLY • link 4.5 years ago by annaA ▴ 10

Login before adding your answer.