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Hi Zhenxing,
I split the positive strand into a.fwd.bam, then I use a.fwd.bam to call m6A motif. I get 109757 peaks totally, and about 20% of them are located in the negative strand. In addition, t…
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Hi,
I am trying ot use IPO on 15 files on a cluster to speed up the process. However IPO keep crashing on our cluster. I tried 16 cores with 8 Go of RAM with should be more than enough for an optim…
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**Is your feature request related to a problem? Please describe.**
Not a problem, just a gap in the tools universe. When modeling both 13C and 1H chemical shifts using ORCA, I'd like to be able to s…
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I just made all peak calling on replicates, pool and pseudoreps. I am now calling the homer idr using:
`python /home/emilie/homer-idr/homer-idr/idr/run_idr.py idr -p peaks/replicates/* -pr peaks/ps…
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Returning, "Each lower bound must be strictly less than each upper bound."
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So the width (on the RT-axis) for molecules could be helpful to determine if there is a "drift/smear". Maybe we could provide this for each hill and derive the needed information from it.
Also sinc…
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Hi!
The README is wrong about::
docker pull peaks:latest
seems to be:
docker pull r4yan2/peaks:latest
The https://hub.docker.com/r/r4yan2/peaks states some commands, which won't work:
ln…
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Hello, I was wondering whether finding quantiles of peaks from a numerical threshold of 1 without an IgG control is the same as calling SEACR with a range of numerical thresholds. For example, instead…
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Hello,
When enableSegmentDragging(true) is set, segment will not detect whether endTime is out of range.
https://github.com/user-attachments/assets/15087faf-98e3-427a-a49d-45e58f94c0c7
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Greetings,
Thank you so much for your amazing work!
I was wondering if there are any options of applying a filter on the peaks that are being used for predicting the motifs from. Currently, TF-M…