Getting gene level readcount from the Asereadcounter GATK tool

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4.2 years ago

hemantcnaik • 0

Hello any one suggest me how to get gene level allele count from the Asereadcounter from GATK

Thank you

RNA-Seq rna-seq R sequence SNP • 1.4k views

ADD COMMENT • link updated 2.6 years ago by fu_entomology ▴ 40 • written 4.2 years ago by hemantcnaik • 0

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Please provide complete information when asking new questions. You seem to have omitted the fact that you are working with single cell RNAseq data ( Mapping percentage require for single cell allele specific analysis ), if this question is a follow-up. What you are asking for is likely not possible to do. I don't recall if you clarified what kind of single cell data you are using in previous posts.

ADD REPLY • link 4.2 years ago by GenoMax 147k

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I am working on mouse dataset from smart seq2 I used Asereadcounter for allelic analysis and how to process the output file to get gene level allele count

ADD REPLY • link 4.2 years ago by hemantcnaik • 0

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You can check out MBASED, which should be compatible with the outputs from ASEReadCounter. For more detailed usage, check out their vignette. I'm not sure if this method is applicable to single-cell data though.