Changes between Version 8 and Version 9 of SOPs/atac_Seq
- Timestamp:
- 08/11/20 11:24:36 (4 years ago)
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SOPs/atac_Seq
v8 v9 86 86 * post-alignment filtering: remove mito/ChrM reads, remove duplciates, remove mapping artifacts: < 38bp and fragments > 2kb, and discordant reads 87 87 * The nucleosome free region (NFR) should be > 38bp to < 147 bases (one nucleosome); mono nucleosome fragments are in the range of 147-200 bp 88 * unless you have high coverage, e.g. ~50M reads or more,use all reads for downstream analysis and not remove mono-, di-, tri-, etc. nucleosome fragments or reads. Otherwise, you may miss many open chromatin regions during peak calling.88 * unless you have high coverage, use all reads for downstream analysis and not remove mono-, di-, tri-, etc. nucleosome fragments or reads. Otherwise, you may miss many open chromatin regions during peak calling. 89 89 * recommend at least ~50M reads/coverage for calling open/accessible regions, and ~200M reads for TF/footprinting. 90 90 * check fragment size distribution (from ATACSeqQC)
