How to select the reads with a certain adapter in a fastq file in R
I am currently doing a paired-end SMART-seq(an low input method of RNA-seq) data. I am interested in selecting the reads with SMART-Seq unique adapter ( 5' end adapter).
I am trying to do the job in R. I can use the Bioconductor tool, ShortRead to read the fastq file, then I can extract the read sequences and convert it to a vector. Then I can detect the reads with the adapter and pick them up by stringr. But definitely, I can't convert the vector back to the fastq file and to do any downstream analysis.
Anyone knows how to select reads with a certain adapter in a fastq file? is there any R tool can achieve this job?
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