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Dear Guanjue,
Thanks for inventing such great software which is quite helpful.
But nowadays when I tried to normalize a 4-sample single-end ATAC-seq data by S3norm. The result is weird, I can't find…
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Hi! Thanks for the cool tool!
When I start from estimated read counts from a different pipeline (STAR > featureCounts) should I provide Taiji with raw reads or should I normalise them somehow before …
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Hi,
I have a question of using scGPT on ATAC data. The typical scATAC-seq has binarized values 0 and 1, so how to make the ATAC counts as bins? Should we only make the counts to only 2 bins: 0-bin an…
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Describe the bug
pipeline because javax.net.ssl.SSLException failed
OS/Platform
OS/Platform: [e.g. Ubuntu 18.04, Google Cloud, Stanford Sherlock/SCG cluster, ...]
Conda version: conda 22.9.0…
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Hi,I am using the scATAC seq data from your article 'Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19'. The effect of using Signac software for …
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## **Describe the bug**
We're trying to reproduce the results described in the paper: https://doi.org/10.1016/j.ajhg.2018.08.001. The experiments are listed here https://www.ncbi.nlm.nih.gov/sra?term…
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I have installed snakepipes and downloaded ATACseq example for test run. However, the example does not run as I expected.
I first run following the suggestion from command.sh and get this:
#####
(s…
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I am trying to train ChromBPNet on Arabidopsis ATAC-seq data, but run into the error `"Input file shifts inconsistent"` as in #153, #174 and #176. Having read through these other issues, I was able to…
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I am struggling to understand, why the "Filter Option: Remove PCR duplicates” in the Genrich tool is set to "Yes" after running the MarkDuplicates tool with “If true do not write duplicates to the out…
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Hi Allen,
This is Tommy. I was trying to connect with you on Linkedin :) I know you rewrote Lisa and you have some script built-in to calculate the regulatory potential score (RP).
Given a bed …