Hi Bin,
The reply given for this same question posted at seqanswers is correct,
including the Tool Shed comments:
http://seqanswers.com/forums/showthread.php?t=14106
To give a bit more detail, when using the public Galaxy instance at
http://usegalaxy.org, the idea would be to run the "NGS: QC and
manipulation -> Clip" tool with each adapter, one at a time. Each time
start with the same original file and only output sequences that are
clipped. Then merge at the end, if wanted, for downstream analysis.
The Clip tool is sourced from the FASTX-toolkit and currently does only
work for 3' adapters. You may want to contact the tool author Assaf
Gordon if you have a suggestions/use cases for tool enhancements
http://hannonlab.cshl.edu/fastx_toolkit/.
Just so you know, there are tools that simply trim off bases, from
either end, which may or may not work for needs. Please see "FASTQ
Trimmer" and "Trim sequences".
I also opened a bitbucket ticket to track the ideas for expanding the
options for this type of function. This can be tracked at:
http://bitbucket.org/galaxy/galaxy-central/issue/659/expand-adapter-sequence-clipping-options
Hopefully one of the available options will work out for your project,
Best,
Jen
Galaxy team
On 9/14/11 2:17 PM, Binbin You wrote:
Hi All,
In " Clip adapter sequences" option of Penn State Galaxy, I choose
"Enter custom sequence" under "Source", and I can only enter One custom
clipping sequence. So how can I enter another 3 adapter sequences which
I want to clip.
In addition, In "*What it does" it shows: *
This tool clips adapters from the 3'-end of the sequences in a
FASTA/FASTQ file.
So how could i do if I have the adapter sequences like this:
5' TACACTCTTTCCCTACACGACGCTCTTCCGATCT
5 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA
5' GACGGCATACGAGCTCTTCCGATCT
5' AGATCGGAAGAGCTCGTATGCCGTC
Thanks very much for any response!
Best wishes,
Bin
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
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