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 converter

followed by

Collapse sequences
On 19 September 2011 09:54, Kevin Lam <kevin@aitbiotech.com> wrote:
For 1) you may refer to
Simulated Dataset of Solexa - SEQanswers

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