Changes between Version 5 and Version 6 of SOPs/atac_Seq


Ignore:
Timestamp:
08/11/20 11:07:43 (4 years ago)
Author:
thiruvil
Comment:

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  • SOPs/atac_Seq

    v5 v6  
    8585//Based on presentation by H.Liu at BioC 2020 presentation //
    8686  *  post-alignment filtering: remove mito/ChrM reads, remove duplciates, remove mapping artifacts: < 38bp and fragments > 2kb, and discordant reads
    87     * The NRF should be > 38bp to < 147 bases (one nucleosome); mono nucleosome fragments are in the range of 147 -200 bp
     87    * The NRF should be > 38bp to < 147 bases (one nucleosome); mono nucleosome fragments are in the range of 147-200 bp
    8888    * don't recommend to remove di-, tri nucleosome fragments for downstream analysis unless you have a great number of reads. Otherwise the you might miss many open chromatin regions during peak calling.
    8989  * check fragment size distribution (from ATACSeqQC)