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Genome annotation (gene names) missing in IGV session file #168

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ktrns opened this issue Feb 17, 2022 · 1 comment
Open

Genome annotation (gene names) missing in IGV session file #168

ktrns opened this issue Feb 17, 2022 · 1 comment
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enhancement New feature or request

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@ktrns
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ktrns commented Feb 17, 2022

Hi there,

We noticed that it would be very useful to have the genome annotation already loaded to the IGV session file that is generated by the pipeline. At the moment, this is missing, and it is saved somewhere in the work directory.

Can this perhaps be added in future?

Thank you for your work
Katrin
@drpatelh drpatelh added the enhancement New feature or request label Nov 15, 2022
@drpatelh drpatelh added this to the 2.0 milestone Nov 15, 2022
@drpatelh
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Hi @ktrns ! I intentionally left the GTF out from being loaded automatically by IGV because it can take quite a long time to load, especially for the larger genomes. Maybe we can load the gene BED file up instead in the future which should load up quicker 🤔

@drpatelh drpatelh removed this from the 2.0 milestone Nov 18, 2022
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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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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@ktrns @drpatelh