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pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
http://stream.pinellolab.org
GNU Affero General Public License v3.0
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Is log transformation and normalization required here? #76

Closed sylestiel closed 4 years ago

sylestiel commented 4 years ago

Dear Huidong Chen, I'm analyzing scATAC data. Can you comment on whether I should upload the zscores-scaled.tsv.gz or the zscores.tsv.gz (generated using the 10X cell ranger output) for the Web browser supported STREAM GUI. In either case do i need to check Log2Transformation and Normalization radio button(s) when running the analysis. Thank you! SH

huidongchen commented 4 years ago

Hi SH,

For scATAC-seq, you should not use log2 transformation or normalization since the zscores have negative values.

Also I would strong recommend that you check out our tutorial notebooks https://github.com/pinellolab/STREAM#tutorial. STREAM web GUI is a simplified version of STREAM package and it might not be sufficient for a solid scATAC-seq analysis.

sylestiel commented 4 years ago

Thank you immensely for your feedback. SHOn June 9, 2020 at 2:01 PM Huidong Chen notifications@github.com wrote:  Hi SH,For scATAC-seq, you should not use log2 transformation or normalization since the zscores have negative values.Also I would strong recommend that you check out our tutorial notebooks https://github.com/pinellolab/STREAM#tutorial. STREAM web GUI is a simplified version of STREAM package and it might not be sufficient for a solid scATAC-seq analysis.—You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or unsubscribe.