comparison between STARsolo and cellranger
Entering edit mode
10 days ago

Good morning , I want to ask you if we can say that cellranger and STARsolo generated to same output in my case. Thank you

cellranger count:

Estimated Number of Cells,Mean Reads per Cell,Median Genes per Cell,Number of Reads,Valid Barcodes,Sequencing Saturation,Q30 Bases in Barcode,Q30 Bases in RNA Read,Q30 Bases in UMI,Reads Mapped to Genome,Reads Mapped Confidently to Genome,Reads Mapped Confidently to Intergenic Regions,Reads Mapped Confidently to Intronic Regions,Reads Mapped Confidently to Exonic Regions,Reads Mapped Confidently to Transcriptome,Reads Mapped Antisense to Gene,Fraction Reads in Cells,Total Genes Detected,Median UMI Counts per Cell


Number of Reads,66601887
Reads With Valid Barcodes,0.975878
Sequencing Saturation,0.708407
Q30 Bases in CB+UMI,0.93492
Q30 Bases in RNA read,0.903313
Reads Mapped to Genome: Unique+Multiple,0.960811
Reads Mapped to Genome: Unique,0.886128
Reads Mapped to Gene: Unique+Multiple Gene,NoMulti
Reads Mapped to Gene: Unique Gene,0.547856
Estimated Number of Cells,1229
Unique Reads in Cells Mapped to Gene,34657887
Fraction of Unique Reads in Cells,0.949836
Mean Reads per Cell,28200
Median Reads per Cell,25194
UMIs in Cells,9615582
Mean UMI per Cell,7823
Median UMI per Cell,6860
Mean Gene per Cell,2129
Median Gene per Cell,2003
Total Gene Detected,20047
STARsolo cellranger • 267 views
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cellranger uses STAR to align the data:

You will want to run STARsolo with parameters recommended by author in this thread:


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