ATAC-seq problem with STAR - Multimapping reads

Question

[Rafael Soler]

Hi,

I have a doubt with STAR in ATAC-seq analysis. When I have performed the alignment, i have obtained I big amount of multi-mapping reads. Now I need this data for ATAC-seq, and I do not know if I have to remove all the multimapping reads, an keep only the Uniquely mapped reads, or allow STAR to put the default option of MAX 10 locus that a read can align to be considered good mapping and stay in the SAM file.

                            UNIQUE READS:
           Uniquely mapped reads number |   15689415
                Uniquely mapped reads % |   51.99%
                  Average mapped length |   98.45
               Number of splices: Total |   9626
    Number of splices: Annotated (sjdb) |   0
               Number of splices: GT/AG |   4180
               Number of splices: GC/AG |   159
               Number of splices: AT/AC |   34
       Number of splices: Non-canonical |   5253
              Mismatch rate per base, % |   0.22%
                 Deletion rate per base |   0.01%
                Deletion average length |   1.57
                Insertion rate per base |   0.01%
               Insertion average length |   1.38
                     MULTI-MAPPING READS:
Number of reads mapped to multiple loci |   12343702
     % of reads mapped to multiple loci |   40.90%
Number of reads mapped to too many loci |   82088
     % of reads mapped to too many loci |   0.27%

Answer 1

[ATpoint]

There is to my knowledge no established and accepted way to deal with multimappers beyond simply discarding them. This is typically done by applying a MAPQ threshold since multimappers usually get low MAPQs. I personally filter for MAPQ > 20 (bowtie2), check the STAR manual on MAPQs since there is no standard on how aligners calculate them. I guess 20 would work for STAR as well, e.g. samtools view -o filtered.bam -q 20 in.bam

[Rafael Soler]

Thank you!! I will test with Bowtie2

[ATpoint]

Please do not simpy close questions. If solved consider to upvote and accept one or many (if present) answer that were helpful.