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,


Dr. Michael Walter
MFT Services
University of Tübingen
Calwerstr. 7
72076  Tübingen

Tel.: +49 7071 29 83210
Fax. + 49 7071 29 5228
web: www.mft-services.de

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