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?
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
Read_1_Sequencing_Primer_3_to_5 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT Read_2_Sequencing_Primer_3_to_5 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Using leeHom tool.
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%