Hi,
I'm trying to create a GTEx-like barChart and boxplot in UCSC Genome Browser for my data. I followed the instructions on the UCSC help page. The trackhub loads without an error. I can see the barChart in the browser. However, if I click on the barChart, I'm not getting the boxplot. Instead I get an error that says Error creating boxplot from sample data. I dont know what the error is. Can someone help me with this? I'm posting the header of my matrix and category text files.
matrix.txt
Name Samp1 Samp2 Samp3 Samp4 Samp5
Sox17 0 0 0 0 0
Mrpl15 0 0 0 0 0
Lypla1 1.7074123012126 1.59300264994819 0 0 0
Tcea1 1.7074123012126 0 0 0 0
Rgs20 0 0 0 0 0
Atp6v1h 0 0 0 0 0
Rb1cc1 0 0 0 0 0
4732440D04Rik 0 0 0 0 0
/
categories.txt
samp1 WT
samp2 WT
samp3 Treatment1
samp4 Treatment1
samp5 Treatment2
1 answer
I emailed this issue to UCSC and I heard back from them almost immediately. It was a very silly error. I'm posting this here just in case someone has a similar error
This was the line from my trackDb file
Track scRNA-Seq superTrack on show shortLabel scRNA-Seq longLabel This track contains expression data from single cell RNA-seq
track data
type bigBarChart
visibility full
shortLabel scRNA-seq
longLabel Expression data from single cell RNA-seq
parent scRNA-Seq on
barChartBars Cluster0 Cluster1 Cluster2 Cluster3 Cluster4 Cluster5 Cluster6 Cluster7 Cluster8
barChartColors #AAAAFF #64B2CE #DA5724 #CBD588 #673770 #D3D93E #38333E #6DDE88 #599861
barChartLabel Clusters
barChartMetric median
barChartUnit Normalized UMI
bigDataUrl http://165.122.23.6/ucsc/JZ_scrna/new/data.bigBed
barChartMatrixUrl http://165.122.23.6/ucsc/JZ_scrna/new/matrix.txt
barChartSampleUrl http://165.122.23.6/ucsc/JZ_scrna/new/categories.txt
barChartUnit has 2 words "Normalized UMI". Making it a single word "Normalized_UMI" fixed the issue
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