Dear Peter, Thanks for the quick reply. But yes, the groomer output was marked as fastqsanger. I changed to generic fastq and back and it didn't work either way. I only get the fasta files from my history as possible input files. However, using the local installation via command line seemed to work (fastx_clipper -a TGGAATTCTCGGGTGCCAAGG -l 15 -n -v -i s_1_sequence.txt -o s_1_sequence_clipped.txt)
Kind regards, 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 prohibited. -----Ursprüngliche Nachricht----- Von: "Peter Cock" <p.j.a.c...@googlemail.com> Gesendet: 17.02.2011 11:44:01 An: "Michael Walter" <michael.wal...@med.uni-tuebingen.de> Betreff: Re: [galaxy-user] FastX Clipper on FastQ data >On Thu, Feb 17, 2011 at 10:06 AM, Michael Walter ><michael.wal...@med.uni-tuebingen.de> 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 > >Hi Mike, > >Is your input FASTQ file definitely marked as type fastqsanger (not just >fastq)? > >The fasta_clipper.xml says it will take >fasta,fastqsanger,fastqsolexa,fastqillumina and is >(now) aware that it should use the -Q 33 switch on Sanger FASTQ, see: >https://bitbucket.org/galaxy/galaxy-central/src/default/tools/fastx_toolkit/fastx_clipper.xml > >Notice however that it does not accept the generic "fastq" Galaxy >format (which I think >would also include color-space FASTQ). > >Peter _______________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
