Forum: Bioinformatics
03-18-2012, 11:05 AM
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Replies: 1
Views: 4,108
edgeR Normalization question
The edgeR manual gives us three examples for DE analysis with each example normalizing the data in different manner.
In the case study 1, the Normalization was done by calcNormFactors. In the case...
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Forum: Bioinformatics
03-06-2012, 09:47 AM
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Replies: 0
Views: 1,351
Multiple Alignment of miRNAs with Precursors
Hi I am looking for a program that can align all miRNA variants or isomirs to the precursers and produce a map like below. Can you please suggest a program for that? thanks in advance.
...
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Forum: Bioinformatics
02-04-2012, 11:47 AM
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Replies: 5
Views: 4,405
Simon, this precisely is my question. The...
Simon, this precisely is my question. The function 'getVarianceStabilizedData' uses 'cds' as the argument which doesnt have same structure as argument 'd' generated by EdgeR. My question is how to...
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Forum: Bioinformatics
02-03-2012, 04:14 PM
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Replies: 5
Views: 4,405
EdgeR: Heatmaps
Hi, I know DESeq can make some really nice heat maps along with clustering of the differentially expressed genes. How can I make such maps with edger? Can I import edgeR data to Deseq to make those...
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Forum: Bioinformatics
01-20-2012, 12:57 PM
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Replies: 23
Views: 64,854
No I meant "if ((FDR < 0.085) AND (p.value <...
No I meant "if ((FDR < 0.085) AND (p.value < 0.05))...no "fishing" or "fishy" business here. I am genuinely curious, how would any one sets the cutoff? There is no consensus in published literature...
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Forum: Bioinformatics
01-20-2012, 12:01 PM
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Replies: 23
Views: 64,854
edgeR: How important is the FDR value?
Hi,
I was wondering if any one can answer my question about FDR
How exactly we should determine the cutoff limit for FDR value? Is 0.1 acceptable or 0.2? Because the number of significantly...
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Forum: Bioinformatics
12-23-2011, 08:57 PM
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Replies: 3
Views: 2,788
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Forum: Bioinformatics
12-14-2011, 10:45 AM
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Replies: 2
Views: 5,425
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Forum: Bioinformatics
12-02-2011, 12:17 PM
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Replies: 2
Views: 2,748
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Forum: Bioinformatics
12-01-2011, 02:29 PM
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Replies: 2
Views: 2,748
Bowtie memory error
Hi - I am getting following error with bowtie
"Error: Could not allocate ChunkPool of 67108864 bytes
terminate called after throwing an instance of 'int'"
Our computer has 12 GB memory with...
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Forum: Bioinformatics
11-30-2011, 03:54 PM
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Replies: 2
Views: 2,546
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Forum: Bioinformatics
11-30-2011, 12:16 PM
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Replies: 2
Views: 2,546
cufflinks error
Hi I am comparing two Bam files with cuffdiff but I get the following error.
Error: sort order of reads in BAMs must be the same
I use bowtie to produce sam files, convert them to bam and sort...
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Forum: Bioinformatics
11-28-2011, 11:15 PM
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Replies: 19
Views: 15,003
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Forum: Bioinformatics
11-22-2011, 09:35 AM
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Replies: 8
Views: 12,892
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Forum: Bioinformatics
11-21-2011, 10:20 AM
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Replies: 8
Views: 12,892
FastQC Problem
Hi while using FastQC, I am getting following error.
uk.ac.bbsrc.babraham.FastQC.Sequence.SequenceFormatException: ID line didn't start with '@'
at...
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Forum: Bioinformatics
11-08-2011, 09:10 AM
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Replies: 4
Views: 1,779
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Forum: Bioinformatics
11-08-2011, 08:40 AM
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Replies: 4
Views: 1,779
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Forum: Bioinformatics
11-07-2011, 10:24 AM
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Replies: 4
Views: 1,779
Multiple Mappings
Hi - I have shortRNA NGS data and there are many short reads that map to multiple types of microRNAs and some microRNAs and genes. To which type of microRNA or gene should I assign this read?
For...
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Forum: Bioinformatics
08-04-2011, 10:38 AM
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Replies: 1
Views: 3,969
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Forum: Bioinformatics
06-19-2010, 03:59 PM
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Replies: 11
Views: 11,125
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Forum: Bioinformatics
06-18-2010, 04:31 PM
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Replies: 11
Views: 11,125
Bowtie output to BED format
Hi - Can any one please suggest a method to convert Bowtie output to BED format? Is there a bioperl script or any software for that?
thanks in advance.
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Forum: Bioinformatics
06-12-2010, 10:37 AM
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Replies: 1
Views: 1,765
Bowtie nor mapping to RNA database
Does bowtie recognize only T and not U? When I used RNA database none of my reads mapped to it, but when changed U to T then they mapped. am I missing something? thanks.
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Forum: Bioinformatics
06-02-2010, 02:00 PM
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Replies: 2
Views: 2,647
Bowtie Build 64-bit
Hi - Bowtie itself is very fast, but bowtie-build takes lots of time to build the indexes. Where do I download the 64-bit version of bowtie-build? I cant locate it in the bowtie wesite.
thanks in...
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Forum: Bioinformatics
05-18-2010, 09:38 AM
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Replies: 1
Views: 3,286
Bowtie database index question
Hi
I am trying to map illumina deepsequenced shortRNA transcripts to different types of RNA databases such as miRNA, piRNA, rRNA etc.
Is it a good idea to map the reads separately to each...
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Forum: Bioinformatics
07-31-2009, 08:33 AM
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Replies: 65
Views: 39,181
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