No I believe there isn't sth like that. It should be a simple perl script to get that info or linux grep would help On 20 September 2011 17:43, Daniel Sher <dsher@sci.haifa.ac.il> wrote:

Thanks Kevin - that might work - collapse sequences and then grab the sequence names using "select" (under filter and sort tools). Is there a way to "loop" such a search in order to go through the lines of a long file? I assume there must be something in the workflows but I have never used that feature.

Thanks

Daniel

On 20/09/2011 11:46, 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> 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> 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> 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 Lab +972-4-8288961 email: 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 Lab +972-4-8288961 email: dsher@sci.haifa.ac.il

-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 Lab +972-4-8288961 email: dsher@sci.haifa.ac.il