Forum: Bioinformatics
11-12-2013, 11:34 AM
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Replies: 11
Views: 8,182
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Forum: Bioinformatics
01-10-2013, 07:45 AM
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Replies: 41
Views: 17,212
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Forum: Bioinformatics
11-08-2012, 07:20 AM
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Replies: 13
Views: 5,836
Hi rboettcher,
According to my experience,...
Hi rboettcher,
According to my experience, yes, the numbering is according to the input order. Please verify with the developers directly, though.
You may want to analyze your data with a...
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Forum: Bioinformatics
11-08-2012, 06:19 AM
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Replies: 13
Views: 5,836
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Forum: Bioinformatics
09-07-2012, 04:00 PM
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Replies: 4
Views: 4,134
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Forum: Bioinformatics
09-07-2012, 06:40 AM
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Replies: 12
Views: 4,903
Hi,
I just want to add that we need to also...
Hi,
I just want to add that we need to also consider the potential sources of the duplication. Is it due to high coverage or PCR-amplification during library prep. It is never a clean cut but you...
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Forum: Bioinformatics
09-04-2012, 07:16 AM
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Replies: 2
Views: 1,985
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Forum: Bioinformatics
09-03-2012, 08:29 AM
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Replies: 8
Views: 3,612
Hi Chris,
Please read the paper on...
Hi Chris,
Please read the paper on MetaPhlAn. The authors screened for representative genes in each family/class. If you use a general database, I am not sure if the results are useful or not. I...
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Forum: Bioinformatics
08-31-2012, 12:16 PM
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Replies: 1
Views: 1,107
Oscar,
Take a look at this:...
Oscar,
Take a look at this: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990000/
Best regards,
Douglas
www.contigexpress.com
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Forum: Bioinformatics
08-31-2012, 07:36 AM
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Replies: 8
Views: 3,612
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Forum: Bioinformatics
08-31-2012, 07:34 AM
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Replies: 1
Views: 935
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Forum: Bioinformatics
08-31-2012, 07:25 AM
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Replies: 3
Views: 1,700
Phil,
For the first few question, you need a...
Phil,
For the first few question, you need a simple script to do the calculation based on the gene annotation. Or for a specific genome, all the ORF sequences may already exist in fasta, which...
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Forum: Bioinformatics
08-31-2012, 07:10 AM
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Replies: 2
Views: 1,606
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Forum: Bioinformatics
08-31-2012, 07:06 AM
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Replies: 2
Views: 979
If the nature and time course of your...
If the nature and time course of your intervention are expected to generate new splicing variants or transcripts, you should merge both pre and post gtfs.
Best regards,
Douglas...
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Forum: Bioinformatics
08-31-2012, 06:59 AM
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Replies: 5
Views: 1,550
Ng,
If you have a BAM file aligned with...
Ng,
If you have a BAM file aligned with hg19, use any genome browser (e.g., IGV) and point it to the location for manual examination. I assume you can find the neighboring sequences of that...
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Forum: Bioinformatics
08-31-2012, 06:44 AM
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Replies: 1
Views: 1,961
Dawe,
Depending on what's downstream...
Dawe,
Depending on what's downstream experiment(s), you may focus on the overlapping 100 genes. (I assume you used the same fold/FDR criteria for both programs.) You may also plot them on a...
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Forum: Bioinformatics
08-31-2012, 06:19 AM
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Replies: 2
Views: 1,602
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Forum: Bioinformatics
08-31-2012, 06:13 AM
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Replies: 15
Views: 4,567
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Forum: Bioinformatics
08-29-2012, 04:35 PM
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Replies: 3
Views: 1,498
check this review:...
check this review: http://www.ncbi.nlm.nih.gov/pubmed?term=song%20albrechtsen
Hopefully it is helpful to you.
Best regards,
Douglas
www.contigexpress.com
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Forum: Bioinformatics
08-29-2012, 03:04 PM
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Replies: 8
Views: 3,612
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Forum: Bioinformatics
08-29-2012, 02:53 PM
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Replies: 2
Views: 1,058
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Forum: Bioinformatics
08-29-2012, 02:50 PM
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Replies: 3
Views: 1,207
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Forum: Bioinformatics
08-29-2012, 10:36 AM
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Replies: 1
Views: 1,163
Hi,
The samtools webpage has quite detailed...
Hi,
The samtools webpage has quite detailed explanation on the parameters. Here is the link: http://samtools.sourceforge.net/samtools.shtml.
Best regards,
Douglas
www.contigexpress.com
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Forum: Bioinformatics
08-29-2012, 08:20 AM
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Replies: 3
Views: 1,498
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Forum: Bioinformatics
08-29-2012, 08:15 AM
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Replies: 5
Views: 1,724
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