Changes between Version 29 and Version 30 of SOPs/atac_Seq


Ignore:
Timestamp:
10/27/20 14:47:37 (4 years ago)
Author:
byuan
Comment:

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  • SOPs/atac_Seq

    v29 v30  
    8080The [https://www.encodeproject.org/atac-seq/#standards ENCODE project] has some recommended TSS enrichment scores, depending on the genome.
    8181
    82 In addition to do varies quality controls, [[ https://www.sciencedirect.com/science/article/pii/S240547122030079X | ataqv ]] summarizes QC results into an interactive html page, which also allows you to view multiple samples together.
     82In addition to do varies quality controls, [ https://www.sciencedirect.com/science/article/pii/S240547122030079X ataqv ] summarizes QC results into an interactive html page, which also allows you to view multiple samples together.
    8383
    8484First, run ataqv on each bam file to generate JSON files.
    … …  
    110110mkarv sample1 sample1.ataqv.json.gz
    111111
    112 # I you have multiple samples, you can combine them into a single report. In this case, both sample1 and sample2 will be in the same plots inside folder called "all_samples"
     112# If you have multiple samples, you can combine them into a single report. In this case, both sample1 and sample2 will be in the same plots inside folder called "all_samples"
    113113mkarv all_samples sample1.ataqv.json.gz sample2.ataqv.json.gz
    114114