I am analyzing rna seq data from illumina stranded protocol 126bp -PE , sequences have nextera adapters using cutadapt I trimmed all the sequences but now I have reads with different lengths, also my insert size form picard has weird peaks,  find below has any one experienced this before?
![enter image description here][1]


#EDIT

Apologies I did little more digging around the pipeline and found out that flexbar was used to remove adapters

and the command used was 

flexbar --adapters adapters.file --adapter-trim-end RIGHT --length-dist --threads 12 --adapter-min-overlap 7 --max-uncalled 250 --min-read-length 25 

adapter used 
>Read_1_Sequencing_Primer_3_to_5 
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
>Read_2_Sequencing_Primer_3_to_5
AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC

#Read1
![enter image description here][2]

#Read2![enter image description here][3]

#Using leeHom tool. 

![enter image description here][4]

#log file leeHom

    Total reads :231670526  100%
    Merged (trimming) 22238730      9.59929%
    Merged (overlap) 0      0%
    Kept PE/SR 93263449     40.2569%
    Trimmed SR 0    0%
    Adapter dimers/chimeras 533995  0.230498%
    Failed Key 0    0%

  [1]: https://i.imgur.com/224uGAh.png
  [2]: https://i.imgur.com/cMBpvVe.png
  [3]: https://i.imgur.com/2SmFqfB.png
  [4]: https://i.imgur.com/y4Vl20a.png
If you try leeHom ([https://grenaud.github.io/leeHom/][1]), it can trim adapters and merge overlapping using a Bayesian algorithm so no cutoffs are required. It will produce 3 types of files to map:

 1. [PREFIX].fq.gz	Sequences that were trimmed and merged confidently by leeHom
 2. [PREFIX]_r1.fq.gz	Forward reads that were neither trimmed nor merged confidently by leeHom
 3. [PREFIX]_r2.fq.gz	Reverse reads that were neither trimmed nor merged confidently by leeHo

Map the .fq.gz as single reads and r1/r2 as pairs. To plot the insert size, get pysam and run the following script as such:  python insertSize.py in.bam
 
    #!/usr/bin/python
    
    import pysam
    import sys; 
    
    
    bamInputFile  = pysam.Samfile(sys.argv[1], "rb");
    
    
    for read in bamInputFile:
        if read.is_unmapped :
            continue;
        if read.is_paired :
            if read.is_proper_pair and read.is_read1 :
                print abs(read.template_length);       
        else:
            print len(read.query_alignment_sequence);
                    
    bamInputFile.close();
    
    
    
    


  [1]: https://grenaud.github.io/leeHom/