valid UMIs in STARsolo output?
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2.5 years ago
hamarillo ▴ 80

Hi,

I was wondering if anyone knows where can I find the proportion of reads with valid UMIs ("Fraction of reads with valid UMIs; i.e. UMI sequences that do not contain Ns and that are not homopolymers.") in the output of STARsolo.

I've checked the sample.Solo.out/Gene/Summary.csv file, but I don't think it's in there...

Number of Reads,496387931
Reads With Valid Barcodes,0.982586
Sequencing Saturation,0.598001
Q30 Bases in CB+UMI,0.940222
Q30 Bases in RNA read,0.913062
Reads Mapped to Genome: Unique+Multiple,0.968168
Reads Mapped to Genome: Unique,0.891923
Reads Mapped to Gene: Unique+Multipe Gene,0.537544
Reads Mapped to Gene: Unique Gene,0.491303
Estimated Number of Cells,11448
Unique Reads in Cells Mapped to Gene,231938960
Fraction of Unique Reads in Cells,0.951049
Mean Reads per Cell,20260
Median Reads per Cell,17430
UMIs in Cells,92608099
Mean UMI per Cell,8089
Median UMI per Cell,6916
Mean Gene per Cell,2344
Median Gene per Cell,2105
Total Gene Detected,33661

I don't think it's in the other log/stats files (i.e. the sample.Log.final.out has alignment stats, nothing related to Barcodes or UMIs).

I've checked the portions of the STAR manual that correspond to STARsolo mode and output files, but the logs aren't explained

starsolo single-cell UMIs RNA-seq • 767 views
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