Understand the CellReads.stat file output from STARsolo

[CassandreHeritier]

Hello,

I want to understand the output file Solo.out/GeneFull_Ex50pAS/CellReads.stats from STARsolo with options --soloCellReadStats Standard and --soloFeatures GeneFull_Ex50pAS but I don't find any manual or instruction on the signification of each column, neither in the STAR manual.

The columns are: CB cbMatch cbPerfect cbMMunique cbMMmultiple genomeU genomeM featureU featureM exonic intronic exonicAS intronicAS mito countedU countedM nUMIunique nGenesUnique nUMImulti nGenesMulti

And the file looks like:

I want to know for each read if the read is intronic or exonic type.

Thanks!

[alexdobin]

Hi @CassandreHeritier

This file shows the mapping statistics of reads in each cell.
There is a discussion about these fields here:
#1501 (comment)
Here is the summary:

cbMatch means the number of read that matched the cell barcode,
cbPerfect for the number of perfect match on cell barcode
cbMMunique : number of reads with cell barcodes that map with mismatches to one barcode in the passlist
cbMMmultiple : number of reads with cell barcodes that map with mismatches to multiple barcodes in the passlist

genomeU : number of reads mapping to one locus in the genome
genomeM : number of reads mapping to multiple loci in the genome
featureU : number of reads mapping to one feature (Gene, GeneFull, etc)
featureM : number of reads mapping to multiple features

exonic: number of reads mapping to annotated exons
intronic: number of reads mapping to annotated introns
These are only calculated for --soloFeatures GeneFull_Ex50pAS and/or GeneFull_ExonOverIntron

exonicAS : number of reads mapping antisense to annotated exons
intronicAS : number of reads mapping antisense to annotated introns
These are only calculated for --soloFeatures GeneFull_Ex50pAS

countedU: number of unique-gene reads whose UMIs contributed to counts in the matrix.mtx
countedM: number of multi-gene reads whose UMIs contributed to counts in the matrix.mtx

mito for the number of read mapping on mitochondrial genome

nUMIunique for the total number of counted UMI for unique-gene reads
nGenesUnique for the number of genes for unique-gene reads
nUMImulti for the total number of counted UMI for multi-gene reads
nGenesMulti for the number of genes for multi-gene reads

[CassandreHeritier]

Thank you so much 💯 👍

[huiz0916]

Hi @alexdobin

This file shows the mapping statistics of reads in each cell. There is a discussion about these fields here: #1501 (comment) Here is the summary:

cbMatch means the number of read that matched the cell barcode, cbPerfect for the number of perfect match on cell barcode cbMMunique : number of reads with cell barcodes that map with mismatches to one barcode in the passlist cbMMmultiple : number of reads with cell barcodes that map with mismatches to multiple barcodes in the passlist

genomeU : number of reads mapping to one locus in the genome genomeM : number of reads mapping to multiple loci in the genome featureU : number of reads mapping to one feature (Gene, GeneFull, etc) featureM : number of reads mapping to multiple features

exonic: number of reads mapping to annotated exons intronic: number of reads mapping to annotated introns These are only calculated for --soloFeatures GeneFull_Ex50pAS and/or GeneFull_ExonOverIntron

exonicAS : number of reads mapping antisense to annotated exons intronicAS : number of reads mapping antisense to annotated introns These are only calculated for --soloFeatures GeneFull_Ex50pAS

countedU: number of unique-gene reads whose UMIs contributed to counts in the matrix.mtx countedM: number of multi-gene reads whose UMIs contributed to counts in the matrix.mtx

mito for the number of read mapping on mitochondrial genome

nUMIunique for the total number of counted UMI for unique-gene reads nGenesUnique for the number of genes for unique-gene reads nUMImulti for the total number of counted UMI for multi-gene reads nGenesMulti for the number of genes for multi-gene reads

Thanks for explanations. nUMIunique means all the umi without de-duplicate or has removed duplication?