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Does nf-core/atacseq apply an offset to each ATAC-seq fragment? #164

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rcorces opened this issue Sep 22, 2021 · 3 comments
Open

Does nf-core/atacseq apply an offset to each ATAC-seq fragment? #164

rcorces opened this issue Sep 22, 2021 · 3 comments
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question Further information is requested
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2.0

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@rcorces
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rcorces commented Sep 22, 2021

Does the pipeline apply the standard +4/-5 offsets to aligned reads to account for the precise Tn5 binding site? I have not been able to find this in the documentation or in the code base.
@gkanogiannis
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I am also interested in this question.

@drpatelh drpatelh added the question Further information is requested label Nov 15, 2022
@drpatelh drpatelh added this to the 2.0 milestone Nov 15, 2022
@jeremymsimon
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Now that v2.0 has come out, I'm curious if this was implemented yet? It seems pretty standard for ATACseq reads to be shifted in this way, such that chromap I believe does it by default. Could we get an update and expected timeline on this to be added?

@jeremymsimon
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Tagging @drpatelh - could we get an update on the above?

ktrns added a commit to ktrns/atacseq that referenced this issue Jun 27, 2023
@ktrns
Fixed nf-core#164 - Introduced 4/5bp shift as it is common for ATAC-s…
dac4367 
…eq data. Fixed nf-core#168 - Always write out genome fa and fai so IGV session file can be opened.
ktrns added a commit to ktrns/atacseq that referenced this issue Jul 3, 2023
@ktrns
Merged ktrns/master into ktrns/dev. Fixed nf-core#164 (4/5 bp shift), f…
f14eeb8 
…ixed nf-core#168 (write genome fa and fai for IGV), fixed nf-core#169 (peak calling).
@ktrns ktrns mentioned this issue Jul 5, 2023
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@samuelruizperez samuelruizperez mentioned this issue Aug 22, 2023
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bjlang added a commit that referenced this issue Sep 6, 2023
@bjlang
Revert "DO NOT MERGE yet: Discuss fixes of #164 #168 #169 "
1030a66
JoseEspinosa added a commit that referenced this issue Sep 6, 2023
@JoseEspinosa
Merge pull request #333 from nf-core/revert-301-dev
e034e1e 
Revert "DO NOT MERGE yet: Discuss fixes of #164 #168 #169 "
bjlang added a commit that referenced this issue Sep 6, 2023
@bjlang
Revert "DO NOT MERGE yet: Discuss fixes of #164 #168 #169 "
17cc561
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@gkanogiannis @rcorces @drpatelh @jeremymsimon