I have a query about using Trimmomatic on PE MiSeq data. I am receiving what seems to be quite low paired returns. Is this typical and/or can anyone suggest what the problem might be -- Input Read Pairs: 982783 Both Surviving: 346732 (35.28%) Forward Only Surviving: 635840 (64.70%) Reverse Only Surviving: 17 (0.00%) Dropped: 194 (0.02%). See the code run below. The problem does appear to be the adapter trimming rather than the quality trimming (as if I remove the adapter trimming step PE returns increases to > 60 %.
Can anyone offer any advice?
TrimmomaticPE: Started with arguments: /home/otills/data/all/140331_C1CR_M01145_0120_000000000-A6UJV_1_IL-TP-014_1.sanfastq.gz \
ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:2 MINLEN:20
Multiple cores found: Using 8 threads
Using PrefixPair: 'TACACTCTTTCCCTACACGACGCTCTTCCGATCT' and 'GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT'
ILLUMINACLIP: Using 1 prefix pairs, 0 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Quality encoding detected as phred33
Input Read Pairs: 982783 Both Surviving: 346732 (35.28%) Forward Only Surviving: 635840 (64.70%) Reverse Only Surviving: 17 (0.00%) Dropped: 194 (0.02%)
TrimmomaticPE: Completed successfully