In processing raw fastq reads, I need to use trimming tools from the Bioconductor ShortRead package, and vcountpattern from Biostrings. It seems impossible to move between the two. I have tried:
- writeFastq to export the trimmed data and importing with readDNAStringSet. Error in .Call2("read_XStringSet_from_fastq", filexp_list, nrec, skip, : read_XStringSet_from_fastq(): FASTQ files with variable sequence lengths are not supported yet
- DNAStringSet(my trimmed data) Error in as.character.default(x) : no method for coercing this S4 class to a vector
- vcountpattern(my trimmed data) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘vcountPattern’ for signature ‘"ShortReadQ"’
- trimLRPatterns(my raw fastq data read as a DNAStringSet) Returns no error, but I have not been able to make this trim my data as does trimTailw from ShortRead.
I realize that there is likely a simple fix, but I am very frustrated that I cannot move between packages. ANy help would be appreciated.