diff --git a/doc/misc/.~lock.Guidelines_ATAcseq_analysis.pptx# b/doc/misc/.~lock.Guidelines_ATAcseq_analysis.pptx#
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-,christian,christian,08.08.2018 14:11,file:///home/christian/.config/libreoffice/4;
\ No newline at end of file
diff --git a/doc/misc/Alignment_issues_Bowtie2 b/doc/misc/Alignment_issues_Bowtie2
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-
-ALIGNMENT AND WORKFLOW
-
-CHARLES bowtie2 settings: Send reminder email
-
-
-TODO: Run -nodovetail run and compare results: How often does dovetailing happen?
-
-
-no-mixed: By default, when bowtie2 cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior.
-
---no-discordant: By default, bowtie2 looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior.
-
-
-Allow one mate alignment to contain another: False
-
-Allow mate alignments to overlap: False
-
-Overlapping and containing ok for an alignment to be concordant, dovetailing not ok
- See http://www.cureffi.org/2012/12/19/forward-and-reverse-reads-in-paired-end-sequencing/ for a nice discussion