Question: Fastx Clipper On Fastq Data
7.0 years ago by
Michael Walter • 20
Michael Walter • 20 wrote:
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 -- 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 Confidentiality Note: This message is intended only for the use of the named recipient(s) and may contain confidential and/or proprietary information. If you are not the intended recipient, please contact the sender and delete the message. Any unauthorized use of the information contained in this message is prohibite d.
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