Forum: Bioinformatics
06-09-2015, 02:56 PM
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Replies: 0
Views: 1,090
Testing a force topology in mrBayes
Hello Everybody,
I have a question related to "Testing a topological hypothesis". I have
tried to run the same procedure as mentioned in the tutorial in order to
check whether two species form...
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Forum: Bioinformatics
06-02-2015, 08:23 AM
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Replies: 1
Views: 995
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Forum: Bioinformatics
04-01-2015, 02:54 AM
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Replies: 2
Views: 1,371
See :-...
See :- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3493127/
https://www.biostars.org/p/77756/
http://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/
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Forum: Bioinformatics
03-24-2015, 07:37 AM
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Replies: 4
Views: 4,527
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Forum: Bioinformatics
03-17-2015, 07:18 AM
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Replies: 2
Views: 1,784
Hello xunong
Hypergeometric distribution is...
Hello xunong
Hypergeometric distribution is used in case of microarray data.
Are you using RNAseq data? If yes- then i would suggest to use GOseq R package. You can create your own GO instance...
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Forum: Bioinformatics
03-06-2015, 08:23 AM
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Replies: 1
Views: 1,466
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Forum: Bioinformatics
03-04-2015, 09:47 AM
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Replies: 1
Views: 1,466
De-novo assembly PASA annotation
Hello Everyone,
We have recently generated two de-novo transcriptomics assembly for two different but related species. These new transcripts seem quite good on the basis of quality measurements,...
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Forum: Bioinformatics
09-24-2014, 01:07 AM
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Replies: 3
Views: 7,127
Please see...
Please see https://blast.ncbi.nlm.nih.gov/BLAST_guide.pdf. Especially page number 9 and question 4.9.
I hope this helps.
Thanks,
Reema
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Forum: Bioinformatics
09-22-2014, 08:10 AM
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Replies: 3
Views: 7,127
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Forum: Bioinformatics
09-22-2014, 08:04 AM
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Replies: 1
Views: 2,249
Hello,
Please see this link :-...
Hello,
Please see this link :- http://seqanswers.com/forums/showthread.php?t=46711. Well I was also very much confused about singleton. As rick mentioned in this post that align reads without...
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Forum: Bioinformatics
09-22-2014, 07:54 AM
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Replies: 4
Views: 7,061
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Forum: Bioinformatics
09-18-2014, 02:43 AM
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Replies: 4
Views: 7,061
Hi Rick,
Thanks for explaining this so...
Hi Rick,
Thanks for explaining this so clearly. It means When we align reads back to the new assembly, and in the alignment summary reads having only one pair e.g only left pair align and only...
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Forum: Bioinformatics
09-17-2014, 03:09 AM
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Replies: 4
Views: 7,061
What is Singletons?
Dear Friends,
I would like to ask :- What is Singletons especially in a de-novo transcriptomics assembly? I known this sound silly:), but I am really very eager to known the exact information...
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Forum: Bioinformatics
09-15-2014, 01:19 AM
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Replies: 7
Views: 3,379
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Forum: Bioinformatics
09-12-2014, 07:47 AM
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Replies: 7
Views: 3,379
Hello kbradnam
Thanks for sharing the link....
Hello kbradnam
Thanks for sharing the link. But i have one more quick question.
partial score is higher than complete score from both assembly(generated from two different samples). As far as...
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Forum: Bioinformatics
09-11-2014, 07:02 AM
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Replies: 7
Views: 3,379
Hello peromhc and kbradnam,
Thank you very...
Hello peromhc and kbradnam,
Thank you very much for your reply. Sorry for getting back late- As I first want to run cegma on my assembly before posting the reply. Here's the update:-
1) CEGMA...
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Forum: Bioinformatics
08-31-2014, 01:30 PM
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Replies: 7
Views: 3,379
CEGMA - FATAL ERROR when running local map 6400
Hello Everyone,
I am trying to get the CEGMA score for our new transcriptome assembly. But when I tried to run cegma on my assemled transcripts, I am getting following error:-
"RUNNING:...
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Forum: Bioinformatics
03-05-2014, 07:27 AM
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Replies: 2
Views: 2,150
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Forum: Bioinformatics
02-27-2014, 03:03 AM
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Replies: 11
Views: 2,591
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Forum: Bioinformatics
02-27-2014, 02:59 AM
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Replies: 2
Views: 2,150
Picard SamToFastq strange behavious
Dear all,
I am using picard SamtoFastq in oredr to convert BAM/SAM to fastq. I have a paired end sample. I am using following command:-
java -jar SamToFastq.jar INPUT=input.bam...
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Forum: Bioinformatics
02-27-2014, 02:49 AM
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Replies: 2
Views: 2,388
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Forum: Bioinformatics
02-13-2014, 08:37 AM
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Replies: 6
Views: 2,011
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Forum: Bioinformatics
02-13-2014, 08:36 AM
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Replies: 2
Views: 2,388
Trinity-Duplicate removal
Dear All,
I am using trinity for transcriptomics assembly. I have few queries:-
1) have two condition(Control and Treated) and each condition has 4 replicates. so if I merge these .fq files...
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Forum: Bioinformatics
02-13-2014, 08:13 AM
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Replies: 6
Views: 2,011
Trinity-Duplicate removal
Dear All,
I am using trinity for transcriptomics assembly. I have few queries:-
1) have two condition(Control and Treated) and each condition has 4 replicates. so if I merge these .fq files...
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Forum: Bioinformatics
02-12-2014, 09:58 AM
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Replies: 17
Views: 10,517
Trinity-duplicate removal
Dear All,
I am using trinity for transcriptomics assembly. I have few queries:-
1) have two condition(Control and Treated) and each condition has 4 replicates. so if I merge these .fq files...
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