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
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