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serenolopezdarwin / apanalysis

Analyze 3'UTR usage in single-cell data.
MIT License
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The required input file “3pseq.bed” #3

Closed ShannonDing7 closed 2 years ago

ShannonDing7 commented 2 years ago

The pipeline is really inspiring and useful! But I have a problem. How is the required input file “3pseq.bed” generated and also the “mouse_median_expr.txt”? Is “3pseq.bed” the merged bed file of the 14 bed files from GSE52528?

vagarwal87 commented 2 years ago

If you could find Sereno's Princeton address and send a joint email to him and me (vikram.agarwal {at} sanofi {dot} com), we could learn how 3pseq.bed is generated. As for mouse_median_expr.txt, this was generated by using a large matrix of gene expression values across many samples in the mouse, and then taking the median expression level across samples to get 1 value per gene. It can be found in Agarwal & Shendure Cell Reports 2020. If you need one or both files, we're happy to provide them to you after you email us.

ShannonDing7 commented 2 years ago

Thanks very much in advance for your kind help!