<!channel> sorry, just wondering if anyone is runn...
# mnaseseqm
Maxime Garcia
12/13/2024, 12:53 PM<!channel> sorry, just wondering if anyone is running this pipeline, I might have found a person interested in continuing the development of this pipeline (or at least trying to update to DSL2)
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Sunil
12/13/2024, 12:57 PMHi, it's me from Discord you were talking to.
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Maxime Garcia
12/13/2024, 12:58 PMHi @Sunil nice to see you here
Maxime Garcia
12/13/2024, 12:59 PMWe have the #C027CM7P08M channel that can be of help if you have specific questions
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Sunil
12/13/2024, 1:00 PMWonderful!! Thanks for pointing out. I'll ping in case I'm stuck at some point (most likely will)
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Maxime Garcia
12/13/2024, 1:10 PMand if you need to talk with other devs, we have #C04QR0T3G3H
Maxime Garcia
12/13/2024, 1:11 PMplease do not hesitate to ask any questions, as I often say, there are #C043FMKUNLB
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Theodoros Georgomanolis
12/13/2024, 1:30 PMsorry for the stupid question, but how is this one different from the rnaseq pipeline?
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Maxime Garcia
12/13/2024, 1:39 PMit's DNA sequencing data obtained via micrococcal nuclease digestion
Maxime Garcia
12/13/2024, 1:41 PMSo different input data, so I'm guessing different tools for preprocessing and analyzing
Maxime Garcia
12/13/2024, 1:41 PM(I'm not familiar at all)
Maxime Garcia
12/13/2024, 1:41 PMAnd there are #C043FMKUNLB, I just said it 😉
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Theodoros Georgomanolis
12/13/2024, 1:42 PMOh my god, I really need new glasses. It is MNaseSeq, not mRNAseq.
disregard my question please.
It's been a while since I seen an MNase seq. I think that most people use ATAC-seq deep sequencing instead of MNase.
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chase mateusiak
05/28/2025, 3:32 PM@Maxime Garcia and @Sunil, I am interested in this workflow, in particular for Chec-seq. Has there been any development on the DSL2 transition?
chase mateusiak
05/28/2025, 4:16 PMwow. Looking at the code now. This is ancient
chase mateusiak
05/28/2025, 4:17 PMancient
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Maxime Garcia
05/28/2025, 4:22 PMI haven't checked on @Sunil in a while I'm afraid
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chase mateusiak
05/28/2025, 4:25 PMok -- I'm looking over this now. I * might * be able to work on it for the rest of this week. It looks like you and Harshil are the original authors? Any bandwidth for a big code review if i can swing it?
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Maxime Garcia
05/28/2025, 4:26 PMOut sick today, on vacation tomorrow, but happy to have a look on anything on Friday
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chase mateusiak
05/28/2025, 4:26 PMim sorry -- feel better!
I'm sure that I wouldn't have anything ready until then, anyway
chase mateusiak
05/28/2025, 10:41 PMafter looking through this more, it isn't really what I need...
ChEC-seq uses MNase, but quite differently than MNase seq for nucleosome occupancy. Unfortunately other than the read qc and alignment, it doesn't share downstream analysis tools.
That isn't a bad thing necessarily -- easy enough to put in an option to use one 'important place finding' tool vs the other -- but logically I'm not sure it is right to group these two datatypes together (despite the fact that I came here since ChEC-seq is broadly an MNase method)
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