The analysis indicators for Smart-seq2 seem abnormal.

[hai178912522]

STAR --runThreadN 16 \
     --genomeDir sheep/geneome/STAR/ \
     --runDirPerm All_RWX \
     --readFilesCommand zcat \
         --outSAMtype None \
         --soloType SmartSeq \
         --readFilesManifest s1.mapfile \
     --soloUMIdedup Exact --soloStrand Unstranded \
         --limitOutSJcollapsed 10000000 --soloCellFilter None \
     --soloFeatures Gene GeneFull --soloOutFileNames output/ features.tsv barcodes.tsv matrix.mtx --outReadsUnmapped Fastx

cat Barcodes.stats noNoAdapter 0 noNoUMI 0 noNoCB 0 noNinCB 0 noNinUMI 0 noUMIhomopolymer 0 noNoWLmatch 0 noTooManyMM 0 noTooManyWLmatches 0 yesWLmatchExact 20223089 yesOneWLmatchWithMM 0 yesMultWLmatchWithMM 0 GeneFull cat Summary.csv Number of Reads,20223089 Reads With Valid Barcodes,1 Sequencing Saturation,0.184216 Q30 Bases in RNA read,0.905109 Reads Mapped to Genome: Unique+Multiple,0.00719257 Reads Mapped to Genome: Unique,0.000716359 Reads Mapped to GeneFull: Unique+Multiple GeneFull,0.00217988 Reads Mapped to GeneFull: Unique GeneFull,0.00217988 cat Features.stats noUnmapped 20077633 noNoFeature 82069 MultiFeature 19303 subMultiFeatureMultiGenomic 18407 noTooManyWLmatches 0 noMMtoWLwithoutExact 0 yesWLmatch 44084 yessubWLmatchExact 44084 yessubWLmatch_UniqueFeature 44084 yesCellBarcodes 1 yesUMIs 35963

Gene cat Summary.csv Number of Reads,20223089 Reads With Valid Barcodes,1 Sequencing Saturation,0.2 Q30 Bases in RNA read,0.905109 Reads Mapped to Genome: Unique+Multiple,0.00719257 Reads Mapped to Genome: Unique,0.000716359 Reads Mapped to Gene: Unique+Multiple Gene,2.47242e-07 Reads Mapped to Gene: Unique Gene,2.47242e-07 cat Features.stats noUnmapped 20077633 noNoFeature 145451 MultiFeature 0 subMultiFeatureMultiGenomic 0 noTooManyWLmatches 0 noMMtoWLwithoutExact 0 yesWLmatch 5 yessubWLmatchExact 5 yessubWLmatch_UniqueFeature 5 yesCellBarcodes 1 yesUMIs 4

I am comparing sheep genomes, and I feel that the Reads Mapped to Genome: Unique is a bit low. Is this normal?

[alexdobin]

Something went very wrong in this run, I would recommend mapping a few reads from one file without single cell options.