{
  "id": 455350,
  "title": "scATAC-seq integration",
  "url": "/competitions/open-problems-single-cell-perturbations/discussion/455350",
  "author_name": "",
  "post_date": "2023-11-14T10:41:04.465321100Z",
  "votes": 8,
  "comment_count": 2,
  "views": 0,
  "content": "<p>Hi everyone, I'm currently working on integrating ATAC-seq data following the Signac tutorial. I was wondering if anyone has experience with this process and could provide some insights. Specifically, I'm trying to follow the multiomics tutorial, and I'm finding it a bit challenging to interpret the results. If anyone could share their expertise or offer guidance on how to interpret the integrated data, I would greatly appreciate it. Thank you!</p>",
  "messages": [
    {
      "id": "2524548",
      "postDate": "11/14/2023 10:41:04",
      "content": "<p>Hi everyone, I'm currently working on integrating ATAC-seq data following the Signac tutorial. I was wondering if anyone has experience with this process and could provide some insights. Specifically, I'm trying to follow the multiomics tutorial, and I'm finding it a bit challenging to interpret the results. If anyone could share their expertise or offer guidance on how to interpret the integrated data, I would greatly appreciate it. Thank you!</p>",
      "rawMarkdown": "Hi everyone, I'm currently working on integrating ATAC-seq data following the Signac tutorial. I was wondering if anyone has experience with this process and could provide some insights. Specifically, I'm trying to follow the multiomics tutorial, and I'm finding it a bit challenging to interpret the results. If anyone could share their expertise or offer guidance on how to interpret the integrated data, I would greatly appreciate it. Thank you!",
      "votes": null
    },
    {
      "id": "2525090",
      "postDate": "11/14/2023 19:16:47",
      "content": "<p>I've encountered an issue with the NucleosomeSignal function from Signac while working with this data. It appears that the function doesn't perform optimally when the widths are around 800 bp. Is this a common challenge, and do you have any suggestions on how to address it effectively?</p>\n<p>On a related note, if anyone is interested in providing insights or comments on the integration of ATAC-seq data, I'm open to discussions. Feel free to reach out, and let's explore this together.</p>",
      "rawMarkdown": "I've encountered an issue with the NucleosomeSignal function from Signac while working with this data. It appears that the function doesn't perform optimally when the widths are around 800 bp. Is this a common challenge, and do you have any suggestions on how to address it effectively?\n\nOn a related note, if anyone is interested in providing insights or comments on the integration of ATAC-seq data, I'm open to discussions. Feel free to reach out, and let's explore this together.",
      "votes": null
    },
    {
      "id": "2525725",
      "postDate": "11/15/2023 10:00:33",
      "content": "<p>Because, from what I understand, we have \"peaks\". So, in order to analyze most of ATAC-seq pipelines, we need the fragments file. How could we obtain it? Can anybody help me on that?</p>",
      "rawMarkdown": "Because, from what I understand, we have \"peaks\". So, in order to analyze most of ATAC-seq pipelines, we need the fragments file. How could we obtain it? Can anybody help me on that?",
      "votes": null
    }
  ],
  "comments": [
    {
      "id": 2525090,
      "author_name": "rogercasals",
      "author_url": "",
      "post_date": "11/14/2023 19:16:47",
      "content": "<p>I've encountered an issue with the NucleosomeSignal function from Signac while working with this data. It appears that the function doesn't perform optimally when the widths are around 800 bp. Is this a common challenge, and do you have any suggestions on how to address it effectively?</p>\n<p>On a related note, if anyone is interested in providing insights or comments on the integration of ATAC-seq data, I'm open to discussions. Feel free to reach out, and let's explore this together.</p>",
      "votes": null,
      "replies": []
    },
    {
      "id": 2525725,
      "author_name": "rogercasals",
      "author_url": "",
      "post_date": "11/15/2023 10:00:33",
      "content": "<p>Because, from what I understand, we have \"peaks\". So, in order to analyze most of ATAC-seq pipelines, we need the fragments file. How could we obtain it? Can anybody help me on that?</p>",
      "votes": null,
      "replies": []
    }
  ],
  "raw_markdown_by_id": {
    "2524548": "Hi everyone, I'm currently working on integrating ATAC-seq data following the Signac tutorial. I was wondering if anyone has experience with this process and could provide some insights. Specifically, I'm trying to follow the multiomics tutorial, and I'm finding it a bit challenging to interpret the results. If anyone could share their expertise or offer guidance on how to interpret the integrated data, I would greatly appreciate it. Thank you!",
    "2525090": "I've encountered an issue with the NucleosomeSignal function from Signac while working with this data. It appears that the function doesn't perform optimally when the widths are around 800 bp. Is this a common challenge, and do you have any suggestions on how to address it effectively?\n\nOn a related note, if anyone is interested in providing insights or comments on the integration of ATAC-seq data, I'm open to discussions. Feel free to reach out, and let's explore this together.",
    "2525725": "Because, from what I understand, we have \"peaks\". So, in order to analyze most of ATAC-seq pipelines, we need the fragments file. How could we obtain it? Can anybody help me on that?"
  },
  "source": "meta"
}