Forum: Bioinformatics
06-27-2013, 05:16 PM
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Replies: 0
Views: 1,682
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Forum: Bioinformatics
09-26-2011, 09:23 AM
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Replies: 2
Views: 2,295
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Forum: De novo discovery
05-18-2011, 04:58 PM
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Replies: 82
Views: 48,139
This is something I am wondering: is there any...
This is something I am wondering: is there any way to come up with an RPKM-like measure of expression level when doing de novo transcriptome assembly? Counting the number of reads per contig (cDNA)...
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Forum: De novo discovery
05-17-2011, 10:37 AM
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Replies: 82
Views: 48,139
Very interesting thread. I am collecting...
Very interesting thread. I am collecting information about the best strategy to perform de novo transcriptome assembly for a plant for which we have no reference genome. From what I read here it...
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Forum: Bioinformatics
03-23-2011, 03:11 PM
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Replies: 2
Views: 15,803
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Forum: Bioinformatics
03-21-2011, 03:44 PM
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Replies: 12
Views: 6,944
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Forum: Bioinformatics
03-02-2011, 04:14 PM
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Replies: 2
Views: 2,295
Dreaded (because unresolved) bad_alloc error
Greetings,
I run into a 'std::bad_alloc()' error when processing a 500MB BAM file with cufflinks on a 8BG machine. The exact error message is
. . .
> Processed 17748 loci. ...
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Forum: Bioinformatics
03-02-2011, 08:39 AM
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Replies: 11
Views: 8,178
I got the same error message with a BAM file of...
I got the same error message with a BAM file of about 500 MB on a 4-CPU machines with 12 GB RAM. It is a 64 bits Linux distribution (kernel 2.6.18); I will try to launch the same cufflink job on my...
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Forum: Bioinformatics
03-01-2011, 10:58 AM
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Replies: 5
Views: 22,046
I found an answer for question (4):...
I found an answer for question (4): http://seqanswers.com/forums/showthread.php?p=13800#post13800
The suggestion from Cole Trapnell is indeed to pool samples with cuffcompare in step 4, then run...
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Forum: Bioinformatics
03-01-2011, 10:46 AM
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Replies: 5
Views: 22,046
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Forum: Bioinformatics
03-01-2011, 10:41 AM
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Replies: 10
Views: 6,007
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Forum: Bioinformatics
03-01-2011, 08:45 AM
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Replies: 10
Views: 6,007
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Forum: Bioinformatics
02-28-2011, 10:15 AM
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Replies: 5
Views: 22,046
Typical TopHat/Cufflinks pipeline?
Greetings,
I am new to RNA-seq analysis, and am trying to understand the high-order logic of the bowtie/tophat/cufflinks/cuffcompare/cuffdiff pipeline. As far as I understand, a typical run would be...
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Forum: Bioinformatics
02-28-2011, 09:03 AM
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Replies: 10
Views: 6,007
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Forum: RNA Sequencing
02-24-2011, 10:38 AM
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Replies: 5
Views: 5,609
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