Forum: Bioinformatics
09-25-2015, 03:40 PM
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Replies: 5
Views: 4,022
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Forum: Bioinformatics
06-16-2015, 11:01 AM
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Replies: 4
Views: 1,543
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Forum: Bioinformatics
06-16-2015, 10:32 AM
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Replies: 4
Views: 1,543
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Forum: Bioinformatics
06-15-2015, 05:26 PM
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Replies: 4
Views: 1,543
HTSeq count to expression level
Hi,
I understand that the raw HTSeq output is number of reads mapped to each gene (correct me if I'm wrong). Is there an easy way of converting counts to gene expression? The method should take...
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Forum: Bioinformatics
05-07-2015, 12:07 PM
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Replies: 9
Views: 1,601
Hi mbblack, I think expression level can be...
Hi mbblack, I think expression level can be correlated with function and particular proteins, due to their function, may have very low gene expression level and/or protein expression level because...
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Forum: Bioinformatics
05-07-2015, 10:05 AM
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Replies: 9
Views: 1,601
Thanks for all of the responses. To me, this...
Thanks for all of the responses. To me, this sounds like it's coming from personal experience of looking at multiple tissue specific profiles. I am wondering if any prior papers have delve into this...
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Forum: Bioinformatics
05-06-2015, 09:52 PM
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Replies: 9
Views: 1,601
Actually I mean if there are any prior research...
Actually I mean if there are any prior research in what types of protein/genes are typically low expressing. For example, we know housekeeping genes are typically always on and expressed in cell at...
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Forum: Bioinformatics
05-06-2015, 12:23 PM
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Replies: 9
Views: 1,601
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Forum: Bioinformatics
12-08-2014, 01:38 PM
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Replies: 13
Views: 3,049
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Forum: Bioinformatics
12-05-2014, 10:27 PM
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Replies: 13
Views: 3,049
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Forum: Bioinformatics
12-05-2014, 07:52 PM
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Replies: 13
Views: 3,049
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Forum: Bioinformatics
12-05-2014, 06:24 PM
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Replies: 13
Views: 3,049
Version number is 0.1.19-4428cd
It...
Version number is 0.1.19-4428cd
It looks like no temporary files are created. The command throws the error message after less than a minute of running (actually I'm not sure how long it...
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Forum: Bioinformatics
12-05-2014, 05:14 PM
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Replies: 13
Views: 3,049
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Forum: Bioinformatics
12-05-2014, 12:40 PM
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Replies: 13
Views: 3,049
indexing tophat bam files
Hi,
I am having trouble using samtools to index my tophat output for IGV viewing. The tophat output bam should be sorted (although I am having trouble too using samtools to sort the tophat output...
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Forum: Bioinformatics
10-21-2014, 03:22 PM
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Replies: 4
Views: 1,191
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Forum: Bioinformatics
10-21-2014, 12:52 PM
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Replies: 4
Views: 1,191
DESeq2 bizarre error - dates in gene list
Hey guys, I am running into a really weird problem in my RNA-seq analysis pipeline. In my final DESeq2 output, in the first column where the gene names are, there are a few entries that are purely...
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Forum: RNA Sequencing
09-08-2014, 01:48 PM
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Replies: 5
Views: 1,425
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Forum: RNA Sequencing
09-08-2014, 12:56 PM
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Replies: 5
Views: 1,425
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Forum: Bioinformatics
09-07-2014, 10:54 AM
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Replies: 6
Views: 4,213
Hi Devon, so what I am trying to do is to use...
Hi Devon, so what I am trying to do is to use DESeq2 to compare two data manipulation methods. The same RNAseq fastq dataset was used in tophat. Condition1 used coverage search (which takes a lot...
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Forum: Bioinformatics
09-06-2014, 02:31 PM
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Replies: 6
Views: 4,213
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Forum: Bioinformatics
09-06-2014, 11:39 AM
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Replies: 6
Views: 4,213
DESeq2 error
Hi all,
New to DESeq2 and getting error consistently while running this line:
dds <- DESeq(dds)
The error message:
estimating size factors
estimating dispersions
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Forum: Bioinformatics
08-27-2014, 09:00 PM
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Replies: 3
Views: 1,412
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Forum: Bioinformatics
08-27-2014, 06:18 PM
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Replies: 3
Views: 1,412
Illumina HiSeq2500 data
I am trying to determine the method used to generate my RNAseq data. On the Illumina website, the read length are either 1*36bp or 2*50bp. My fastq reads are non-strand-specific and non-paired...
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