Some reads do not seem to be assigned to genes correctly by starsolo

[zhouyiqi91]

STAR Version 2.7.11

Starsolo performs perfectly on human and mouse samples. However, it performs strangely on a Saccharomyces_cerevisiae sample. I found that the number of reads assigned to features is low:

*.Solo.out/GeneFull_Ex50pAS/Features.stats

                                        noUnmapped        1511309
                                       noNoFeature       18090383
                                      MultiFeature        6065952
                       subMultiFeatureMultiGenomic        6015439
                                noTooManyWLmatches              0
                              noMMtoWLwithoutExact              0
                                        yesWLmatch       24094716
                                yessubWLmatchExact       21910936
                       yessubWLmatch_UniqueFeature       24094716
                                   yesCellBarcodes         823115
                                           yesUMIs       23008164

However, using featureCounts to quantify the same BAM output by Starsolo can yield much higher assigned reads.

Assigned        39880594
Unassigned_Unmapped     0
Unassigned_Read_Type    0
Unassigned_Singleton    0
Unassigned_MappingQuality       0
Unassigned_Chimera      0
Unassigned_FragmentLength       0
Unassigned_Duplicate    0
Unassigned_MultiMapping 15937496
Unassigned_Secondary    0
Unassigned_NonSplit     0
Unassigned_NoFeatures   3967801
Unassigned_Overlapping_Length   0
Unassigned_Ambiguity    551624

This is an example of a read that is assigned to YAL038W (XT tag) in featureCounts, but cannot be assigned to the gene in starsolo:

E200025550L1C040R03704342097    0       I       73159   255     150M    *       0       0       CCGTATCAACTTCGGTATTGAAAAGGCTAAGGAATTCGGTATCTTGAAGAAGGGTGACACTTACGTTTCCATCCAAGGTTTCAAGGCCGGTGCTGGTCACTCCAACACTTTGCAAGTCTCTACCGTTTAAAAAAAGAATCATGATTGAAT ?@E<DA;D<>DF@B#@AEEA2>E.7D,CDB<<@A>AB>2@EBDACA<DD4FB@BDD,<@DDB?9CADD:AB?ABAA;>FCBA@B99<E<+;;>EE%A@?DEDFAEAAEDFFB;?CDD?FEB=EAFDBDF>>FED95E;EFEEFAEFFBD? NH:i:1  HI:i:1  nM:i:0  AS:i:148        CR:Z:AGACGTTCA_ATGCCTAAG_AGATCTCGT    UR:Z:TCGCTCTCTCGA        GX:Z:-  GN:Z:-  sF:B:i,7,0      CB:Z:AGACGTTCA_ATGCCTAAG_AGATCTCGT      UB:Z:TCGCTCTCTCGA       XS:Z:Assigned   XN:i:1  XT:Z:YAL038W

A nearby read can be correctly assigned by both featureCounts and starsolo

E200025550L1C029R01701620491    0       I       73142   255     145M5S  *       0       0       ACTGATGATGTTGAAGCCCGTATCAACTTCGGTATTGAAAAGGCTAAGGAATTCGGTATCTTGAAGAAGGGTGACACTTACGTTTCCATCCAAGGTTTCAAGGCCGGTGCTGGTCACTCCAACACTTTGCAAGTCTCTACCGTTTAAAAA FFFFFFFFFFFFFCEFFFFFFFFFFFFFFF@FFFFFFFFFFFEFFFFFFDFFFFCFFFFFFFFFDDFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFF@FFFFFFFFFFFFFFFFGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF NH:i:1  HI:i:1  nM:i:0  AS:i:143        CR:Z:ACACACCAA_CAATGCAAC_CTCTAACAC    UR:Z:TTATGTGCACGG        GX:Z:YAL038W    GN:Z:CDC19      sF:B:i,1,1      CB:Z:ACACACCAA_CAATGCAAC_CTCTAACAC      UB:Z:TTATGTGCACGG       XS:Z:Assigned   XN:i:1 XT:Z:YAL038W

Definition of YAL038W in gtf

I       sgd     gene    71786   73288   .       +       .       gene_id "YAL038W"; gene_name "CDC19"; gene_source "sgd"; gene_biotype "protein_coding";
I       sgd     transcript      71786   73288   .       +       .       gene_id "YAL038W"; transcript_id "YAL038W_mRNA"; gene_name "CDC19"; gene_source "sgd"; gene_biotype "protein_coding"; transcript_name "CDC19"; transcript_source "sgd"; transcript_biotype "protein_coding";
I       sgd     exon    71786   73288   .       +       .       gene_id "YAL038W"; transcript_id "YAL038W_mRNA"; exon_number "1"; gene_name "CDC19"; gene_source "sgd"; gene_biotype "protein_coding"; transcript_name "CDC19"; transcript_source "sgd"; transcript_biotype "protein_coding"; exon_id "YAL038W_mRNA-E1";
I       sgd     CDS     71786   73285   .       +       0       gene_id "YAL038W"; transcript_id "YAL038W_mRNA"; exon_number "1"; gene_name "CDC19"; gene_source "sgd"; gene_biotype "protein_coding"; transcript_name "CDC19"; transcript_source "sgd"; transcript_biotype "protein_coding"; protein_id "YAL038W";
I       sgd     start_codon     71786   71788   .       +       0       gene_id "YAL038W"; transcript_id "YAL038W_mRNA"; exon_number "1"; gene_name "CDC19"; gene_source "sgd"; gene_biotype "protein_coding"; transcript_name "CDC19"; transcript_source "sgd"; transcript_biotype "protein_coding";
I       sgd     stop_codon      73286   73288   .       +       0       gene_id "YAL038W"; transcript_id "YAL038W_mRNA"; exon_number "1"; gene_name "CDC19"; gene_source "sgd"; gene_biotype "protein_coding"; transcript_name "CDC19"; transcript_source "sgd"; transcript_biotype "protein_coding";

starsolo.Log.out.txt
genomeGenerate.Log.out.txt