Get fastq files back from LRPatterns output

Question

[vivekruhela]

I have used trimLRPatterns to trim adapters from WES data. But the output of this bioconductor package is not in fastq format. How to convert the output of trimLRPatterns package (which is DNAStringset) into fastq format so that I can use this result in pipeline.

[h.mon]

Use BBDuk / SeqyClean / Trimmomatic / Cutadapt / whatever package which reads fastq and output fastq. How did you read your WES into R? Why are you using R for this?

[vivekruhela]

I am trying to make my complete pipeline of WES analysis in R using Bioconuctor. So I am trying to figure out which one is better to use from trimLRPatterns or trimmomatic or cutadapt. There are some other packages in Bioconductor for adaptor trimming , I am not sure whether they give results in fastq format. Thanks for your reply.

[vivekruhela]

I amusing the command fastq1 <- sread(readFastq(outfile_temp)) to read sequence from fastq files where the outfile_tmp is the combination of multiple fastq files. this command gives the sequences in DNAStrings formats and I lost fastq formats. So after trimming I want that format again. There are some packages to write fastq files but I am not sure how efficient they are. Thanks