For read simulation, you may also want to give Grinder a try. I made a Galaxy wrapper for it (see in the toolshed: http://toolshed.g2.bx.psu.edu/) Florent On 20/09/11 18:46, Kevin Lam wrote:

Hi Daniel, You would have multiple names for each sequence and that would be quite hard to display. I am sure someone thought through this. Since the sequence is the same, you can use the sequence to look back in the fastq file for read name. Although I am not sure how that would help you?

Cheers Kevin

On 20 September 2011 13:43, Daniel Sher <dsher@sci.haifa.ac.il <mailto:dsher@sci.haifa.ac.il>> wrote:

Thanks Kevin. However, the collapse sequences replaces the original name of the sequences with a numerical code, and I need to keep the original names. Any other suggestions?

Thanks

Daniel

On 20/09/2011 05:32, Kevin Lam wrote:

...

Hi Daniel for 2) you may use the tools under NGS QC and manipulation FASTQ to FASTA <http://main.g2.bx.psu.edu/tool_runner?tool_id=cshl_fastq_to_fasta> converter

followed by

Collapse <http://main.g2.bx.psu.edu/tool_runner?tool_id=cshl_fastx_collapser> sequences

On 19 September 2011 09:54, Kevin Lam <kevin@aitbiotech.com <mailto:kevin@aitbiotech.com>> wrote:

For 1) you may refer to

Simulated Dataset of Solexa - SEQanswers <http://seqanswers.com/forums/showthread.php?t=806>

Has anyone replied you for 2) ?

On 18 September 2011 21:12, Daniel Sher <dsher@sci.haifa.ac.il <mailto:dsher@sci.haifa.ac.il>> wrote:

Hello,

I have two questions - I apologize if they are trivial..

1) I want to simulate the amount of Illumina sequencing needed to sequence and assemble a known genome. Is there a way to randomly pick sequences of a specific length from a genome (either one available online or one I upload)? Something like "pick 100bp randomly (either strand), move 400-500bp forward and pick another 100bp?"

2) Is there a way to remove redundant sequences from a FASTA file without losing the original sequence names (as happens with "collapse")?

Thanks

Daniel

-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Daniel Sher, PhD Department of Marine Biology Leon H. Charney School of Marine Sciences University of Haifa, Mt. Carmel 31905, Haifa, Israel

Office+972-4-8240731 <tel:%2B972-4-8240731> Lab+972-4-8288961 <tel:%2B972-4-8288961> email:dsher@sci.haifa.ac.il <mailto:dsher@sci.haifa.ac.il>

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-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Daniel Sher, PhD Department of Marine Biology Leon H. Charney School of Marine Sciences University of Haifa, Mt. Carmel 31905, Haifa, Israel

Office+972-4-8240731 <tel:%2B972-4-8240731> Lab+972-4-8288961 <tel:%2B972-4-8288961> email:dsher@sci.haifa.ac.il <mailto:dsher@sci.haifa.ac.il>

___________________________________________________________ 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 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/