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lot of multi-maaping-hg_38 genome mapping #2667

@Aastha2000tanu

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@Aastha2000tanu

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.

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