STAR --runThreadN 44
--genomeDir /home/lab/genome_hg38/star_genome_149
--outFileNamePrefix /mnt/f/Reditool_data/547/new_align_547_0.3/aligned547
--outSAMattributes All
--outSAMtype BAM SortedByCoordinate
--outFilterType BySJout
--outFilterMismatchNmax 999
--outFilterScoreMinOverLread 0.3
--outFilterMatchNminOverLread 0.3
--sjdbGTFfile /home/lab/genome_hg38/Gencode_annotation/gencode.v46.annotation.gtf
--readFilesIn /mnt/f/547/LIB095547_22WGHMLT4_S1_L004_R1_001_val_1.fq /mnt/f/547/LIB095547_22WGHMLT4_S1_L004_R2_001_val_2.fq
Started job on | Jul 15 15:11:00
Started mapping on | Jul 15 15:12:30
Finished on | Jul 15 15:57:07
Mapping speed, Million of reads per hour | 70.28
Number of input reads | 52260927
Average input read length | 235
UNIQUE READS:
Uniquely mapped reads number | 5016458
Uniquely mapped reads % | 9.60%
Average mapped length | 246.72
Number of splices: Total | 2017408
Number of splices: Annotated (sjdb) | 1963646
Number of splices: GT/AG | 2000137
Number of splices: GC/AG | 13781
Number of splices: AT/AC | 2204
Number of splices: Non-canonical | 1286
Mismatch rate per base, % | 0.79%
Deletion rate per base | 0.05%
Deletion average length | 2.92
Insertion rate per base | 0.05%
Insertion average length | 2.57
MULTI-MAPPING READS:
Number of reads mapped to multiple loci | 43006432
% of reads mapped to multiple loci | 82.29%
Number of reads mapped to too many loci | 1458211
% of reads mapped to too many loci | 2.79%
UNMAPPED READS:
% of reads unmapped: too many mismatches | 0.00%
% of reads unmapped: too short | 5.23%
% of reads unmapped: other | 0.09%
CHIMERIC READS:
Number of chimeric reads | 0
% of chimeric reads | 0.00%
why there is so many multi loci, please help me in navigating this.
STAR --runThreadN 44
--genomeDir /home/lab/genome_hg38/star_genome_149
--outFileNamePrefix /mnt/f/Reditool_data/547/new_align_547_0.3/aligned547
--outSAMattributes All
--outSAMtype BAM SortedByCoordinate
--outFilterType BySJout
--outFilterMismatchNmax 999
--outFilterScoreMinOverLread 0.3
--outFilterMatchNminOverLread 0.3
--sjdbGTFfile /home/lab/genome_hg38/Gencode_annotation/gencode.v46.annotation.gtf
--readFilesIn /mnt/f/547/LIB095547_22WGHMLT4_S1_L004_R1_001_val_1.fq /mnt/f/547/LIB095547_22WGHMLT4_S1_L004_R2_001_val_2.fq
why there is so many multi loci, please help me in navigating this.