Changes between Version 110 and Version 111 of SOPs/atac_Seq


Ignore:
Timestamp:
04/04/24 10:51:48 (6 weeks ago)
Author:
byuan
Comment:

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  • SOPs/atac_Seq

    v110 v111  
    7474}}}
    7575
    76   * Remove duplicates with Picard's 'MarkDuplicates' or 'samtools rmdup'.
     76  * Remove duplicates with Picard's 'MarkDuplicates' or 'samtools rmdup'. If your sequence depth is exceptionally high, duplicated reads might actually be part of the normal signals, meaning they may not necessarily need to be removed.
    7777{{{
    7878java -jar /usr/local/share/picard-tools/picard.jar MarkDuplicates I=Mapped_reads.bam O=Mapped_reads.noDups.bam M=foo.marked_dup_metrics.txt REMOVE_DUPLICATES=true