Hi List,
I have a couple of miRNA-Seq files (Illumina GAIIx, 29nt read length). These reads contain differing amounts of 3' adapter sequences and therefore map really badly to the human genome (with eland v2). Therefore, I'd like to use the FastX clipper tool, which states that "This tool clips adapters from the 3'-end of the sequences in a FASTA/FASTQ file." However, After uploading my fastq files and converting it to Sanger format, the clipper does not accept the fastq file as input. After converting it to fasta it works fine. However, the mapping tools will only accept fastq files. So my question is, is there a way to clip the adapter directly in the fastq file (we have a local installation of galaxy, so I may also use command line options)?
Thank you very much for your input,
Mike