Questions about TE and Gene quantification

[liuweihahaha]

My process is to send the bam file output by STARsolo to SoloTE, but the output result of SoloTE makes me feel confused.The following is the output result of the SoloTE：

A total of 9074490 UMIs are in the final matrix. Of these, 2580135 (28.433%) correspond to genes. and 6494355 (71.567%) correspond to TEs. TE detected UMIs are distributed as follows: Locus-specific TEs: 5922649 UMIs (91.197%). Subfamily TEs: 571706 (8.803%).

Only 9074490 UMI were counted to the final result. When I looked at the bam file, I found that there were actually 353056107reads in total. The bam file results are as follows：

Started job on | Jun 01 10:58:44 Started mapping on | Jun 01 10:59:03 Finished on | Jun 01 11:29:13 Mapping speed, Million of reads per hour | 702.21

                      Number of input reads |   353056107
                  Average input read length |   150
                                UNIQUE READS:
               Uniquely mapped reads number |   233058988
                    Uniquely mapped reads % |   66.01%
                      Average mapped length |   149.36
                   Number of splices: Total |   151247104
        Number of splices: Annotated (sjdb) |   148955816
                   Number of splices: GT/AG |   149404255
                   Number of splices: GC/AG |   1223002
                   Number of splices: AT/AC |   130002
           Number of splices: Non-canonical |   489845
                  Mismatch rate per base, % |   0.24%
                     Deletion rate per base |   0.01%
                    Deletion average length |   1.79
                    Insertion rate per base |   0.01%
                   Insertion average length |   1.48
                         MULTI-MAPPING READS:
    Number of reads mapped to multiple loci |   95549477
         % of reads mapped to multiple loci |   27.06%
    Number of reads mapped to too many loci |   1072
         % of reads mapped to too many loci |   0.00%
                              UNMAPPED READS:

Number of reads unmapped: too many mismatches | 0 % of reads unmapped: too many mismatches | 0.00% Number of reads unmapped: too short | 23456573 % of reads unmapped: too short | 6.64% Number of reads unmapped: other | 989997 % of reads unmapped: other | 0.28% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00%

[liuweihahaha]

I sincerely hope you can answer this question，Thank you.

[bvaldebenitom]

Hi @liuweihahaha ,

I hope you are doing well.

The difference between UMIs and total number of reads is related to the amplification process carried out for sequencing. Here are 2 resources from 10X Genomics where this is described: https://kb.10xgenomics.com/hc/en-us/articles/115004037743-How-does-Cell-Ranger-correct-for-amplification-bias https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/algorithms/overview

If this is helpful, please proceed to close the issue. If not, let me know of further questions.