Changes between Version 2 and Version 3 of SOPs/HiChIP


Ignore:
Timestamp:
02/02/26 14:17:01 (3 weeks ago)
Author:
gbell
Comment:

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  • SOPs/HiChIP

    v2 v3  
    66=== Analysis outline ===
    77 * [#SetConfig Set up the MAPS configuration file]
    8  * [#Submit Submit data processing to the LSF batch queue]
     8 * [#Submit Submit data processing to the computing cluster]
    99
    1010=== [=#SetConfig Set up the configuration file] ===
    … …  
    1818}}}
    1919
    20 === [=#Submit Submit data processing to the LSF batch queue] ===
     20=== [=#Submit Submit data processing to the computing cluster] ===
    2121
    22 The command below is an example for how to run MAPS and should be used when submitting these computations to the LSF batch queue.  In this example, ChIP peaks are provided to the pipeline, rather than being called by it (using MACS2) and the reference genome (hg19) is for human (-o specifies "organism" here).
     22The command below is an example for how to run MAPS and should be used when submitting these computations to the computing cluster.  In this example, ChIP peaks are provided to the pipeline, rather than being called by it (using MACS2) and the reference genome (hg19) is for human (-o specifies "organism" here).
    2323{{{
    2424Arima-MAPS_v2.0.sh -C 0 -I /path/to/fastqFiles/fastqFileNamePrefix -O /path/to/output -m /path/to/peaks/peaks.bed -o hg19 -b /nfs/genomes/human_gp_feb_09_no_random/bwa_alt_name/hg19.fa -t 8 -f 1