search

harbourlab / SparK

Publication quality NGS track plotting
102 stars 20 forks source link

How to set `normalizeUsing` when using bamCoverage? #17

Closed YiweiNiu closed 2 years ago

YiweiNiu commented 2 years ago

Hi,

Thanks for developing this useful tool.

I have two questions:

  1. How to set normalizeUsing parameter when using bamCoverage from deeptools, if I want to use SparK? Also, should I use the same normalizeUsing method for different types of data, e.g. RNA-seq, ATAC-seq?

  2. For ATAC-seq data, should I use bamCoverage to generate the bedGraph files for SparK, e.g. using the parameter you mentioned bamCoverage -b bamfile.bam -o outputfilename.bdg -bs 1 -of bedgraph?

Bests, Yiwei

harbourlab commented 2 years ago

Hi Yiwi,

I would recommend CPM for both RNA-seq and ATAC-seq. Reason being that you are just looking at reads per million which is fine for a localized area in my option. The more fancy ways of normalizing RNA-seq (e.g. by transcripts per million is more interesting for quantitative studies, but you could to TPM for RNA-seq too if you wanted to.

Hope this helps! Cheers Stefan

Stefan Kurtenbach, Ph.D. Research Assistant Professor Department of Ophthalmology, Bascom Palmer Eye Institute University of Miami Miller School of Medicine Sylvester Comprehensive Cancer Center Director, ISCI Pluripotent Stem Cell Laboratory

Biomedical Research Building Room 913 1501 NW 10th Avenue, Miami, FL 33136 305-243-3892 office, 786-252-4379 cell @.**@.>

On Sep 15, 2021, at 4:49 AM, Niu Yiwei @.**@.>> wrote:

CAUTION: This email originated from outside the organization. DO NOT CLICK ON LINKS or OPEN ATTACHMENTS unless you know and trust the sender.

Hi,

Thanks for developing this useful tool.

I have two questions:

  1. How to set normalizeUsing parameter when using bamCoveragehttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdeeptools.readthedocs.io%2Fen%2Fdevelop%2Fcontent%2Ftools%2FbamCoverage.html&data=04%7C01%7CStefan.Kurtenbach%40med.miami.edu%7C38dcab55dbd14d736a3c08d97825b976%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637672925707184149%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=4k0QKQDuw8qxZRS6XxUu%2F9RvJC8B3rTb6nO6nWjF5mI%3D&reserved=0 from deeptools, if I want to use SparK? Also, should I use the same normalizeUsing method for different types of data, e.g. RNA-seq, ATAC-seq?

  2. For ATAC-seq data, should I use bamCoverage to generate the bedGraph files for SparK, e.g. using the parameter you mentioned bamCoverage -b bamfile.bam -o outputfilename.bdg -bs 1 -of bedgraph?

Bests, Yiwei

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fharbourlab%2FSparK%2Fissues%2F17&data=04%7C01%7CStefan.Kurtenbach%40med.miami.edu%7C38dcab55dbd14d736a3c08d97825b976%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637672925707194140%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=n95u7uBWFfO4meVFYLYCXB43MxuPQtur9Ojvth6YgyU%3D&reserved=0, or unsubscribehttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FAHANDYVN3ATXP4J7DNT2XILUCBMZNANCNFSM5EB5S2EA&data=04%7C01%7CStefan.Kurtenbach%40med.miami.edu%7C38dcab55dbd14d736a3c08d97825b976%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637672925707194140%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=PYVsATi9KeJO3dkcJTSpkXJse%2FfQ3Dox5u8kZgDqIA8%3D&reserved=0. Triage notifications on the go with GitHub Mobile for iOShttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fapps.apple.com%2Fapp%2Fapple-store%2Fid1477376905%3Fct%3Dnotification-email%26mt%3D8%26pt%3D524675&data=04%7C01%7CStefan.Kurtenbach%40med.miami.edu%7C38dcab55dbd14d736a3c08d97825b976%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637672925707204134%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=LpKRmC4yXsY%2FXWNO%2F03o17bSOraoechfNNYAvlO%2Bw%2B4%3D&reserved=0 or Androidhttps://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fplay.google.com%2Fstore%2Fapps%2Fdetails%3Fid%3Dcom.github.android%26referrer%3Dutm_campaign%253Dnotification-email%2526utm_medium%253Demail%2526utm_source%253Dgithub&data=04%7C01%7CStefan.Kurtenbach%40med.miami.edu%7C38dcab55dbd14d736a3c08d97825b976%7C2a144b72f23942d48c0e6f0f17c48e33%7C0%7C0%7C637672925707204134%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gFfkIatoDiUkeS%2Bh9QdfmsNUScsEMGCrNpEISFDWi20%3D&reserved=0.

YiweiNiu commented 2 years ago

Thank you for your prompt reply. Got it now.