I'm using BBduk 38.00 for adaptor trimming on NexteraXT libraries multiplexed with i5 and i7 indices and sequenced on an NextSeq500 2x150:
When I plot the bhist output from BBduk (A, C, G, T, N % at each position on read one then read2), I get strong GC and AT precent divergence over the first 16-18 bp of read 1 and read 2.
It looks like I'm missing some forward primer or transposase sequence and, in fact, the most common bases are similar to the read 2 Nextera transposase sequence.
Here is an example plot:
https://photos.app.goo.gl/hH2UjJ9iErPbC5nP9
Code:
bbduk.sh in=sample.fq.gz ref=adapters.fa bhist=bhist.txt k=23 hdist=1 ktrim='r' overwrite=t mink=8 tbe tbo ftm=5
It looks like I'm missing some forward primer or transposase sequence and, in fact, the most common bases are similar to the read 2 Nextera transposase sequence.
Here is an example plot:
https://photos.app.goo.gl/hH2UjJ9iErPbC5nP9
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