How to avoid trimming the middle part of the reads

[Tianwei]

Dear all,

I am new for this Forum. I have the Truseq paired-end DNA data. Each paired end read contains a PCR specific probe sequence in the fastq files. Now I want to trim these probe sequences off before the alignment. However, since the targeted amplicons are overlapped, some probe sequences are the part of the real amplicon sequences in other reads.

So by providing the probe sequences fasta file, I want to trim or softclip the probe sequence if it is present at the end of a read, but not trim it if it is present in the middle a read which is supposed to be the real amplicon sequence.

Seems "Trimmomatic" or "BBDuk" are popular trimming tools. But I am not sure whether I can limit the trimming only at the ends of the reads.

Any suggestions about this?

[Brian Bushnell]

BBDuk has flags to restrict adapter-trimming operations to only the X bases at the ends of the reads - "restrictleft=X" or "restrictright=X". I'm not sure if this will accomplish exactly what you want, though. Perhaps you could draw a diagram of the different scenarios in which the sequence appears, indicating which part of the read pair should be trimmed in each case?