Forum: Bioinformatics
10-11-2016, 02:12 PM
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Replies: 0
Views: 2,480
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Forum: Bioinformatics
03-30-2016, 02:29 PM
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Replies: 0
Views: 1,422
Samtools is failing to phase bam files accurately
My colleagues and I are assembling transcriptomes from RNASeq data. Our pipeline can (loosely) be outlined as follows:
1. De novo assembly using all RNASeq read data
2. Identification of potential...
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Forum: Bioinformatics
03-30-2016, 01:31 PM
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Replies: 1
Views: 1,495
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Forum: Bioinformatics
02-19-2016, 02:19 PM
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Replies: 1
Views: 2,666
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Forum: Bioinformatics
02-19-2016, 12:21 PM
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Replies: 1
Views: 2,666
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Forum: Bioinformatics
09-18-2015, 02:42 PM
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Replies: 1
Views: 1,282
A good answer to my questions is given here: ...
A good answer to my questions is given here:
https://groups.google.com/forum/#!topic/trans-abyss/_mHXGbtcO_U
MPI allows multi-threading between nodes in a cluster, while standard multi-threading...
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Forum: Bioinformatics
09-17-2015, 04:05 PM
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Replies: 2
Views: 2,529
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Forum: Bioinformatics
09-05-2015, 04:54 PM
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Replies: 0
Views: 1,594
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Forum: Bioinformatics
06-03-2015, 09:26 AM
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Replies: 1
Views: 1,282
MPI and multi-threading in trans-abyss
Can anyone explain to me the difference between MPI processes and multithreading in trans-abyss?
Are the two mutually exclusive alternative forms of parallel processing? (The literature...
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Forum: Bioinformatics
05-26-2015, 05:27 PM
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Replies: 1
Views: 1,939
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Forum: Bioinformatics
05-13-2015, 02:56 PM
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Replies: 0
Views: 2,002
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Forum: Bioinformatics
02-18-2015, 02:57 PM
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Replies: 3
Views: 3,948
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Forum: Bioinformatics
02-07-2015, 10:57 AM
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Replies: 1
Views: 1,939
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Forum: Bioinformatics
02-03-2015, 11:06 AM
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Replies: 0
Views: 2,065
Cuffmerge outputs only exon annotation data
Hi,
I am analyzing RNA-Seq data to discover new genes, exons and polymorphic sites. I recently aligned the RNA of 7 different tissue samples against a reference genome using TopHat, and cleaned up...
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Forum: RNA Sequencing
01-06-2015, 03:41 PM
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Replies: 3
Views: 2,356
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Forum: RNA Sequencing
11-26-2014, 05:37 PM
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Replies: 0
Views: 2,359
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Forum: Bioinformatics
11-17-2014, 06:01 PM
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Replies: 1
Views: 2,549
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Forum: Bioinformatics
10-16-2014, 09:38 AM
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Replies: 0
Views: 2,201
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Forum: Bioinformatics
10-06-2014, 04:22 PM
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Replies: 4
Views: 2,890
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Forum: Bioinformatics
09-24-2014, 04:19 PM
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Replies: 4
Views: 2,890
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Forum: Bioinformatics
08-04-2014, 04:36 PM
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Replies: 1
Views: 1,057
What exactly are "read groups"
I am reading the samtools manual. For the -r and -R flags in the view function, the manual refers to "read groups". I have not been able to work out exactly what read groups are. Can anyone enlighten...
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Forum: Bioinformatics
07-18-2014, 09:13 PM
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Replies: 10
Views: 7,468
Thank you blakeoft. I dropped the PE flag and...
Thank you blakeoft. I dropped the PE flag and added individual file names for each output file and the program executed properly.
NB: I also tried using the -baseout <outputBase> flag rather than...
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Forum: Bioinformatics
07-18-2014, 10:36 AM
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Replies: 10
Views: 7,468
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Forum: Bioinformatics
03-10-2014, 09:46 AM
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Replies: 1
Views: 1,400
Cuffdiff thread option
Can anyone explain to me the following option in CuffDiff:
-p/--num-threads <int>
Use this many threads to align reads. The default is 1.
What are threads? Will it take longer to run the...
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Forum: Bioinformatics
03-10-2014, 09:43 AM
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Replies: 1
Views: 1,437
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