package for ATACseq data analysis

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adR ▴ 40

@do-it-23093

Last seen 4 months ago

Germany, München

Hello everyone,

I am wondering if there is a comprehensive Bioconductor tool with detailed workflow for ATACseq data analysis?

Thank you!

SequencingData ATACSeq ATACseqQC • 1.4k views

ADD COMMENT • link updated 2.3 years ago by Rory Stark ★ 5.2k • written 3.2 years ago by adR ▴ 40

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ATACseqQC is good for ATACseq data post-alignment quality control. For ATAC-seq data analysis workflow, see https://informatics.fas.harvard.edu/atac-seq-guidelines.html. For a pipeline, see esATAC: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6061683/.

Haibo

ADD REPLY • link 3.2 years ago Haibo Liu ▴ 20

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Thank you Haibo for your quick answer! However,

the first function in the esATAC is not working, it gave me an error as follows.

   Error in atacPipe2(case = list(fastqInput1 = system.file(package = "esATAC",  : 
         this function is still under developing

I also did not see any function that could help me to convert sequence reads stored in the BAM file to count matrix for some downstream analysis like differential expression analysis and so on!

Best, Amare

ADD REPLY • link 3.2 years ago adR ▴ 40

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The DiffBind package vignette shows the workflow for obtaining a count matrix and performing a differential analysis of ATAC-seq data.

ADD REPLY • link 2.3 years ago Rory Stark ★ 5.2k

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