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Hi,
1) How can we obtain Divergent and Transition Motifs when analyzing scATAC-seq data using STREAM_scATAC-seq_motifs.ipynb in Jupyter ?
2) For the Leaf Markers how do we intepret the data i…
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I have been successful integrating 3 ATACseq samples using your vignettes and other posts on github.
However, using the final integrated object I get an error when using coverageplot(integrated)
Thi…
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Hi,
Thanks a lot for developing this very useful package. I got an error message when running FindTransferAnchors() to transfer the label from one scATAC data to another scATAC data.
Below is my…
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After integrating the scATAC and scRNA-seq by ArchR, I found a new matrix - GeneIntegrationMatrix. But I don't know what the different compared to GeneScoreMatrix.
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Hi there,
First thanks for a great method and paper. I've recently been looking at integrating scATAC-seq and scRNA-seq datasets for identically prepared but distinct cell populations. In doing so,…
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alling peaks ...
--Using MACS2...
INFO @ Fri, 24 Jul 2020 21:03:22:
# Command line: callpeak -t home/salappa/output/mapping_result/P2_9.positionsort.MAPQ30.bam --outdir output/peaks/MACS2 -n P2_…
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Hello @kdzimm et al.,
Thank you for providing this excellent resource for incorporating a random effect for individual when running MAST for single-cell differential expression analyses. After load…
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Dear Dr. Stuart,
Thank you for developing this amazing tool!
I'm analyzing a scATAC-seq dataset following this tutorial: https://satijalab.org/signac/articles/pbmc_vignette.html
An error occu…
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Hello Taiji Developers,
Happy new year! First off, thank you for making this awesome tool. So this is my first time trying out your tool, and I've run into some unusual errors. See below:
Fo…
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Hi ,
I have 1 actaseq PBMC sample and the same RNASeq sample
I followed the protocol described scATACSEQ: https://satijalab.org/signac/articles/pbmc_vignette.html#integrating-with-scrna-seq-dat…