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Forum: Bioinformatics 10-06-2008, 01:39 PM
Replies: 14
Views: 7,923
Posted By spirit
Yes. That's right. That's the reason why we are...

Yes. That's right. That's the reason why we are developing the new SNP detector of ZOOM. We are adding the SNP detection part considering many elements affects how probably this position is a true...
Forum: Bioinformatics 10-03-2008, 02:10 PM
Replies: 14
Views: 7,923
Posted By spirit
I think MAQ's paper take into account of the...

I think MAQ's paper take into account of the diploid problem. However, I haven't have a try. So I have no idea of what its output looks like.

You can also try apfejes's software. Hi, apfejes,...
Forum: Bioinformatics 10-03-2008, 11:56 AM
Replies: 14
Views: 7,923
Posted By spirit
Yes. MAQ will take two steps to get final SNP...

Yes. MAQ will take two steps to get final SNP results. I agree with apfejes that it's not good to do alignment and SNP calling at the same time, because you need to map all possible reads to one...
Forum: Bioinformatics 10-03-2008, 07:30 AM
Replies: 14
Views: 7,923
Posted By spirit
I think MAQ can deal with Illumina paired-end...

I think MAQ can deal with Illumina paired-end data and output the SNPs. Maybe I misunderstand your meaning of "detects SNP while also taking advantage of the distance information from the paired-end...
Forum: Bioinformatics 08-31-2008, 10:30 AM
Replies: 9
Views: 3,861
Posted By spirit
Maybe you can try ZOOM. It handles *_seq.txt and...

Maybe you can try ZOOM. It handles *_seq.txt and *_prb.txt automatically.
Forum: Bioinformatics 08-21-2008, 07:48 AM
Replies: 2
Views: 3,472
Posted By spirit
Hi, ECO. Nice to meet you! For ABI SOLiD...

Hi, ECO. Nice to meet you!

For ABI SOLiD data, two types of mismatches --- the sequencing errors on color space and the mismatches caused by nucleotide polymorphism, should be differentiated. ...
Forum: Bioinformatics 08-20-2008, 02:32 PM
Replies: 2
Views: 3,472
Posted By spirit
ZOOM released (supporting both Illumina data and ABI SOLiD data)

Hi,

ZOOM is designed to map millions of short reads, emerged by next-generation sequencing technology, back to the reference genomes, and carry out post-analysis.

1. The spaced seed strategy...
Forum: Bioinformatics 08-10-2008, 08:15 PM
Replies: 236
Views: 544,955
Posted By spirit
Hi, Anthony, Sorry for the late reply. I...

Hi, Anthony,

Sorry for the late reply. I was out for weekend. You are THE Anthony Fejes! Your blog enlightened us a lot!!! Thank you! We like it. :)

The results on the benchmark above were...
Forum: Bioinformatics 08-08-2008, 03:39 PM
Replies: 236
Views: 544,955
Posted By spirit
Thank you for your interest. I will answer these...

Thank you for your interest. I will answer these questions as I could.

1. What are the longest and shortest reads it can handle effectively?

Now, ZOOM could handle reads of length ranging from...
Forum: Bioinformatics 08-08-2008, 01:31 PM
Replies: 236
Views: 544,955
Posted By spirit
And may I ask a question? What is the pair-end...

And may I ask a question? What is the pair-end data of Illumina/Solexa data like? ZOOM now accepts two types of pair-end reads input. One is two fasta input files recording reads from two ends...
Forum: Bioinformatics 08-08-2008, 01:23 PM
Replies: 236
Views: 544,955
Posted By spirit
Hi, lh3 and apfejes. Thanks for you opinion on...

Hi, lh3 and apfejes. Thanks for you opinion on ZOOM :). I am one of the developers of ZOOM. In fact, we will release the command-line version of ZOOM next week.

We finished the part of ZOOM...
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