Changes between Version 90 and Version 91 of SOPs/atac_Seq


Ignore:
Timestamp:
08/19/21 16:03:31 (4 years ago)
Author:
thiruvil
Comment:

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  • SOPs/atac_Seq

    v90 v91  
    102102  * If you have human (hg38, hg19) and mouse (mm10, mm9) samples with biological replicates, you run [[https://github.com/ENCODE-DCC/atac-seq-pipeline|ENCODE ATAC-seq Pipeline]]. The pipeline takes fastq files, cleans and maps the reads, filters aligned reads and does peak calls. Here is the [[https://www.encodeproject.org/pipelines/ENCPL787FUN/|schema of the workflow]].  In addition, it does quality controls. Here is a [[http://barc.wi.mit.edu/education/hot_topics/ChIPseq_ATACseq_2021/qc.html | sample QC report]]. The steps below shows you how to run it on our Whitehead server.
    103103      * content in input sample.json:
    104 
    105104{{{
    106105{
    … …  
    131130          * mm9: /nfs/BaRC_datasets/ENCODE_ATAC-seq_Pipeline/mm9/mm9.tsv
    132131          * mm10: /nfs/BaRC_datasets/ENCODE_ATAC-seq_Pipeline/mm10/mm10.tsv
    133 
    134132       * Before running ENCODE pipeline, verify there is no preexisting conda startup code with the command below:
    135133{{{
    136134conda env list
    137135}}}
    138          You have no preexisting conda if you get "conda: command not found". Otherwise, log out, log back in, start the new conda instance, and activate encode-atac-seq-pipeline
    139 
     136      You have no preexisting conda if you get "conda: command not found". Otherwise, log out, log back in, start the new conda instance, and activate encode-atac-seq-pipeline
    140137      * Ignore the developer's instructions, use your home directory for conda and the pipeline.
    141138{{{
    … …  
    144141conda activate encode-atac-seq-pipeline
    145142}}}
    146 
    147143      * Run. Files could be url or fullpath. [[https://github.com/ENCODE-DCC/atac-seq-pipeline/blob/master/docs/input.md | Detail information about .json file]]
    148144{{{
    … …  
    151147conda deactivate
    152148}}}
    153 
    154      * The QC report is call-qc_report/execution/qc.html
    155      * idr peaks files:
     149      * The QC report is call-qc_report/execution/qc.html
     150      * idr peaks files:
    156151           * rep1: call-idr_pr/shard-0/execution/rep1-pr1_vs_rep1-pr2.idr0.05.bfilt.narrowPeak.gz
    157152           * rep2: call-idr_pr/shard-1/execution/rep2-pr1_vs_rep2-pr2.idr0.05.bfilt.narrowPeak.gz