Forum: Bioinformatics
07-10-2011, 10:05 PM
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Replies: 30
Views: 9,565
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Forum: Bioinformatics
05-23-2011, 02:08 AM
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Replies: 3
Views: 1,348
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Forum: Bioinformatics
05-22-2011, 07:53 PM
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Replies: 9
Views: 3,764
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Forum: Bioinformatics
05-22-2011, 07:26 PM
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Replies: 9
Views: 3,764
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Forum: Bioinformatics
03-30-2011, 02:29 AM
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Replies: 1
Views: 1,973
CLIP-seq dataset
Dear All,
I'm currently working on a HITS-CLIP project in our lab, and we wanted to do some comparison with previous projects. However, I just found out that I cannot find/download the datasets...
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Forum: De novo discovery
03-07-2011, 01:14 AM
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Replies: 12
Views: 6,853
in transcriptome, the reads come from many dna...
in transcriptome, the reads come from many dna transcripts, which is why the assembler uses different k-mer sizes to try to assemble them correctly. Meanwhile, in denovo assembly, the reads come from...
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Forum: Bioinformatics
03-07-2011, 12:44 AM
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Replies: 7
Views: 2,681
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Forum: De novo discovery
03-07-2011, 12:42 AM
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Replies: 12
Views: 6,853
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Forum: De novo discovery
03-07-2011, 12:16 AM
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Replies: 12
Views: 6,853
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Forum: Bioinformatics
02-06-2011, 08:15 PM
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Replies: 2
Views: 2,541
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Forum: Bioinformatics
02-01-2011, 12:12 AM
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Replies: 2
Views: 2,541
clustering paired-end reads
Hi Guys,
Anybody can tell me which tools to use for paired-end reads clustering?
In addition, I would like to do the clustering for 5 different datasets.
I looked through UCLUST and CD-HIT,...
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Forum: Introductions
01-30-2011, 07:15 PM
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Replies: 8
Views: 6,009
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Forum: Bioinformatics
01-24-2011, 06:24 PM
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Replies: 12
Views: 7,284
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Forum: Bioinformatics
01-24-2011, 01:55 AM
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Replies: 12
Views: 7,284
I agree that its not an encouraging number,...
I agree that its not an encouraging number, though the problem most likely lies in soap denovo configuration rather than the data itself. I used soap denovo several times and found it a bit hard to...
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Forum: Bioinformatics
01-18-2011, 07:35 PM
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Replies: 3
Views: 2,119
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Forum: Bioinformatics
12-14-2010, 12:08 AM
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Replies: 1
Views: 1,515
It depends on what is your definition of false...
It depends on what is your definition of false positive mapping. Due to repeats, some reads can be mapped into several locations with the same level of quality. One way is to employ some sort of...
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Forum: Bioinformatics
12-13-2010, 12:36 AM
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Replies: 2
Views: 7,297
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Forum: 454 Pyrosequencing
12-12-2010, 08:43 PM
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Replies: 11
Views: 2,533
this...
this (http://www.ncbi.nlm.nih.gov/pubmed/19156205) might be helpful...
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Forum: RNA Sequencing
12-07-2010, 12:47 AM
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Replies: 4
Views: 2,520
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Forum: Bioinformatics
12-07-2010, 12:04 AM
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Replies: 147
Views: 58,988
Hi Kaiye,
interesting tool you got there....
Hi Kaiye,
interesting tool you got there. anyway, have you publish the method? I am curious about one thing, say you have 1 read, you will grow the pattern until you cannot get a match, then you...
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Forum: RNA Sequencing
12-06-2010, 11:46 PM
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Replies: 4
Views: 2,520
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Forum: Bioinformatics
10-25-2010, 08:33 PM
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Replies: 0
Views: 1,310
Ideal Reads for Different NGS Applications
Hi All,
I'm in a position where I need to advice biologists which technology is suitable for their experiment purpose. Is there any study which explores the ideal condition of reads (or rule of...
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Forum: Bioinformatics
10-21-2010, 07:16 PM
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Replies: 3
Views: 2,171
Since you already tried mapping and got few...
Since you already tried mapping and got few alignments, I don't think assembly will produce a better result. However, as francois.sabot said, you can try relaxing the mapping criteria (higher...
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Forum: Metagenomics
10-21-2010, 01:24 AM
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Replies: 12
Views: 6,077
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Forum: Bioinformatics
10-07-2010, 07:20 PM
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Replies: 1
Views: 2,799
Hi, just my 2cents:
"I expect that if...
Hi, just my 2cents:
"I expect that if Bowtie's options are set to only align unique reads with no mismatches, there shouldn't be a difference between whole-genome and single chromosome index...
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