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DO NOT MERGE yet: Discuss fixes of #164 #168 #169 #301
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Dev -> Master for v2.0 release
Remove paired-end option, and use reads as single-end; otherwise, the coverage graph is misleading as it will often span over nucleosomes
…eq data. Fixed nf-core#168 - Always write out genome fa and fai so IGV session file can be opened.
…then be used for TFBS enrichment.
…ixed nf-core#168 (write genome fa and fai for IGV), fixed nf-core#169 (peak calling).
ktrns
changed the title
DO NOT MERGE yet: Discuss fixes of #168 #169
DO NOT MERGE yet: Discuss fixes of #164 #168 #169
Jul 5, 2023
8 tasks
@ktrns , thanks for this! My group is interested to get this going, I will take things from this point, but If you are still working with this pipeline, I would love to catch up so we can coordinate efforts. let me know! |
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Hi guys,
I have just talked to @JoseEspinosa, and we agreed that it would be best to create a pseudo-PR so we can next discuss our suggested changes after the summer break.
Mainly, we have fixed the following issues:
deeptools/alignmentsieve
. At the moment this only works for paired-end data and throws an error if applied to single-end data.It would be fantastic if you could have a look at our changes. We are looking forward to discuss them with you.
Note to you and myself: I haven't adapted documentation yet.
Best wishes & thanks,
@ktrns and @andpet0101