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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