These reads were sequenced (2x100) with Hiseq 2500 rapid mode. In the first pictures, the reads as they were when I got them:
R1
R2
And then I ran trim_galore (0.3.7). I used the reverse complement of the 3'-end of the Nextera® transposase sequence as an adapter sequence:
trim_galore -q 20 --fastqc -a CTGTCTCTTATA --stringency 1 --paired --retain_unpaired --length 50 $1 $2
And this is what the reads look like now:
R1:
R2:
I assume all the bias that is left in the 5' and 3'-ends is due to the cutting preferences of the Nextera transposase. Is this assumption correct, i.e. are my reads clean?
R1
R2
And then I ran trim_galore (0.3.7). I used the reverse complement of the 3'-end of the Nextera® transposase sequence as an adapter sequence:
trim_galore -q 20 --fastqc -a CTGTCTCTTATA --stringency 1 --paired --retain_unpaired --length 50 $1 $2
And this is what the reads look like now:
R1:
R2:
I assume all the bias that is left in the 5' and 3'-ends is due to the cutting preferences of the Nextera transposase. Is this assumption correct, i.e. are my reads clean?
Comment