I am doing adaptor trimming ,its illumina universal adaptor , I using cutadapt to trim the adaptor sequence.

Alignment without adaptor trimming 
 

    Left reads:
              Input     :  46627933
               Mapped   :  29928631 (64.2% of input)
                of these:  11992814 (40.1%) have multiple alignments (8801 have >20)
    Right reads:
              Input     :  46627933
               Mapped   :  29469536 (63.2% of input)
                of these:  11724006 (39.8%) have multiple alignments (8688 have >20)
    63.7% overall read mapping rate.
    
    Aligned pairs:  28562130
         of these:  11404825 (39.9%) have multiple alignments
                      155607 ( 0.5%) are discordant alignments
    60.9% concordant pair alignment rate.

Alignment after adaptor trimming 

    Left reads:
              Input     :  46624601
               Mapped   :  44668679 (95.8% of input)
                of these:  29803908 (66.7%) have multiple alignments (56945 have >20)
    Right reads:
              Input     :  46624601
               Mapped   :  43936907 (94.2% of input)
                of these:  29470503 (67.1%) have multiple alignments (56649 have >20)
    Unpaired reads:
              Input     :       226
               Mapped   :       181 (80.1% of input)
                of these:        95 (52.5%) have multiple alignments (0 have >20)
    95.0% overall read mapping rate.
    
    Aligned pairs:  42110389
         of these:  28673148 (68.1%) have multiple alignments
                    34996114 (83.1%) are discordant alignments
    15.3% concordant pair alignment rate.


Cutadapt command that  used , [reference ][1]

    cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o HL60_trimmed1.fastq -p HL60_trimmed2.fastq FRED_6_150224_BC6BK7ANXX_P1881_1001_1_123bp.fastq FRED_6_150224_BC6BK7ANXX_P1881_1001_2_123bp.fastq 

I m not able to get it how come after trimming of adaptor the concordant rate goes down ?


Any suggestion or help would be highly appreciated .

















       


  [1]: http://cutadapt.readthedocs.io/en/stable/guide.html#trimming-paired-end-reads
Normally when the concordant rate decreases dramatically after adapter-trimming it indicates that pairing was broken, which can happen if the files are trimmed independently and some reads were discarded.  You could try running BBMap's reformat.sh like this:

    reformat.sh in1=trimmed1.fq in2=trimmed2.fq vpair

...to verify that, according to the read names, the reads are still properly paired after trimming.  I don't see anything wrong with your trimming command, though.

In this case, I think the problem might be Tophat2/Bowtie2 calculating concordant pairs incorrectly.  Before trimming, reads with adapters (which fully overlap) probably just did not map at all.  After trimming, the new reads that map would map 100% overlapping; and indeed a lot of the reads that mapped previously with a few mismatches at the end (and not fully overlapping because of the adapter overhang) would also now map fully overlapping.  Perhaps your version of Tophat2/Bowtie2 does not consider that concordant.  I suggest you try a different aligner such as BBMap or Star and see what it reports for the concordance rate.