Distinguishing between single cell and bulk data in recount3 study explorer
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kstachelek • 0
Last seen 3 months ago
United States

Is there any way to filter the recount3 study explorer for single cell versus bulk datasets? I have tried searching with "bulk" and -"single cell" in abstracts. Could there be some additional filtering column for this purpose?

recount3 • 220 views
Entering edit mode
Last seen 22 days ago
United States

Hi @kstachelek,

We have predicted whether samples are bulk or single cell under the recount_pred columns http://rna.recount.bio/docs/raw-files.html#project-level-metadata-files like at:

$ zcat sra.recount_pred.SRP187765.MD.gz | head
rail_id external_id study   sample_acc  curated.type    curated.tissue  pattern.predict.type    pred.type   curated.cell_type   curated.cell_line
2009177 SRR8690542  SRP187765   SRS4458982  NA  NA  rna-seq rna-seq NA  NA
2009206 SRR8690543  SRP187765   SRS4458983  NA  NA  rna-seq rna-seq NA  NA
2009239 SRR8690544  SRP187765   SRS4458984  NA  NA  rna-seq rna-seq NA  NA
2009270 SRR8690545  SRP187765   SRS4458985  NA  NA  rna-seq rna-seq NA  NA
2009303 SRR8690546  SRP187765   SRS4458986  NA  NA  rna-seq rna-seq NA  NA
2009333 SRR8690547  SRP187765   SRS4458987  NA  NA  rna-seq rna-seq NA  NA
2009366 SRR8690548  SRP187765   SRS4458988  NA  NA  rna-seq rna-seq NA  NA
2009396 SRR8690549  SRP187765   SRS4458989  NA  NA  rna-seq rna-seq NA  NA
2009622 SRR8690550  SRP187765   SRS4458990  NA  NA  rna-seq rna-seq NA  NA

Regrettably, we don't have the information for all studies. So we haven't tried to include that information on the study explorer. Also, the curated information was done by one of our co-authors for _some_ studies, not all of them.

Best, Leo


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