Changes between Version 74 and Version 75 of SOPs/atac_Seq


Ignore:
Timestamp:
07/09/21 08:57:44 (4 years ago)
Author:
gbell
Comment:

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  • SOPs/atac_Seq

    v74 v75  
    1717=== [=#preprocess Pre-process reads] ===
    1818
    19   * Check adapter contamination with fastqc. Remove adapters with cutadapt or trim_galore.  Since many ATAC-seq experiments use the Nextera DNA Library Prep Kit, one commonly needs to trim Nextera adapters.
    20 
    21 {{{
    22 # --fastqc                Run FastQC in the default mode on the FastQ file once trimming is complete.
    23 # --nextera               Nextera adapter is commonly used for ATAC-seq
    24                           Adapter sequence to be trimmed is the first 12bp of the Nextera adapter
     19  * Check adapter contamination with fastqc. Remove adapters with cutadapt or trim_galore. 
     20
     21{{{
     22# --fastqc                Run FastQC in the default mode on the fastq file once trimming is complete.
     23# --nextera               Adapter sequence to be trimmed is the first 12bp of the Nextera adapter
    2524                          'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence.
     25                          Since many ATAC-seq experiments use the Nextera DNA Library Prep Kit,
     26                          one commonly needs to trim Nextera adapters.
     27# --paired                If reads are paired, both reads need to pass or they are both removed.
     28# --length                Discard trimmed reads shorter than this length.
     29
    2630trim_galore --fastqc  -nextera --paired --length 30 -o clean_adaptor_folder read1.fq read2.fq
    2731}}}