Barchart download
Vera Kaiser
Hello, I am trying to download the following single cell gene expression track:
https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/kidneyStewart/cell_type.bb
I can download this file, but the data does not include a header which explains column 9, which contains the info about the cell-type-specific expression.
head cell_type.bed
chr1 30266 31109 RP11-34P13.3 0 + ENSG00000243485.3 20 0,0,0,0,0,0,0,0,0,0,0,0.000821283,0,0,0,0,0,2.44913e-05,0,0
chr1 34553 36081 FAM138A 0 - ENSG00000237613.2 20 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
chr1 69090 70008 OR4F5 0 + ENSG00000186092.4 20 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0
I’ve tried via the REST API, but still no success.
For example, curl -X GET http://api.genome.ucsc.edu/getData/track?genome=hg38&track=kidneyStewartCellType&format=barChart
Gives
"error": "extraneous arguments found for function \/getData\/track 'format=barChart'
Any suggestion how I can download the track in a format that includes the info on cell types?
Thanks!
Vera Kaiser, PhD I
Senior Bioinformatician
Working pattern: Monday-Thursday
Roslin Innovation Centre, Easter Bush Campus, Edinburgh EH25 9RG
+44 (0) 131 651 9661
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Clay Fischer
Thank you for your question about single cell expression data in the UCSC Genome Browser.
Some colleagues saw your question and shared that the metadata for these fields is available in the associated ra (relational-alternative) file which contains the metadata for the track:
https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/human/hg38/kidneyStewart.ra
barChartBars ascending_vasa_recta_endothelial_cell B_cell T_cell_CD4+ T_cell_CD8+ connecting_tubule_cell descending_vasa_recta_endothelial_cell epithelial_progenitor_cell fibroblast glomerular_endothelial_cell intercalated_cell mononuclear_phagocyte natural_killer_cell other_immune_cell pelvic_epithelial_cell peritubular_capillary_endothelial_cell podocyte principal_cell proximal_tubule_cell thick_ascending_loop_of_Henle transitional_urothelium_cell
The above metadata defines the order in the track description page:
https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=kidneyStewartCellType
Under the methods section, there is a link to the original data on the Cell Browser, where you can view the dataset in full instead of aggregate pseudo-bulk:
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