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Forum: Bioinformatics 05-03-2013, 12:24 AM
Replies: 0
Views: 1,003
Posted By stephenhart
downloading human conservation scores for genomeGraphs

I have been using genomeGraphs in R ((http://www.bioconductor.org/packages/release/bioc/vignettes/GenomeGraphs/inst/doc/GenomeGraphs.pdf)) and would like to analyze/visualize conservation scores for...
Forum: Bioinformatics 04-30-2013, 06:08 AM
Replies: 0
Views: 1,194
Posted By stephenhart
UCSC human conservation data

I am using GenomeGraphs and want to plot conservation scores alongside human gene regions. In the vignette, they use yeastCons1. Where would I get the equivalent for human?

Thanks.
Forum: Bioinformatics 04-30-2013, 05:06 AM
Replies: 1
Views: 2,695
Posted By stephenhart
count v dispersion plot

I am analyzing my RNA-seq data with cummeRbund. I have four conditions, 5 biological replicates per condition. Why do the count vs dispersion plots look more or less identical for all four...
Forum: Bioinformatics 03-15-2013, 07:16 AM
Replies: 2
Views: 2,924
Posted By stephenhart
gene tracking with cummerBund - persistent problem

Hello. I'm having some difficulty with the makeGeneRegionTrack feature of cummerBund. If I rebuild my cuffData.db with 'mm10_ensGene.gtf', then the following happens:


> cuff <-...
Forum: Bioinformatics 02-24-2013, 01:35 AM
Replies: 1
Views: 1,979
Posted By stephenhart
gene tracking in cummeRbund

Hello,

I am having difficulty with the makeGeneRegionTrack command in cummeRbund. Below is what happens, after rebuilding the cuffData.db with the gtf file downloaded from the cufflinks website....
Forum: Bioinformatics 02-08-2013, 08:13 AM
Replies: 3
Views: 3,199
Posted By stephenhart
Question cummeRbund gene tracking

Hello,

I am having an issue with gene tracking in cummeRbund. The following happens:

> genetrack <- makeGeneRegionTrack(myGene)
Error in `[.data.frame`(features(object), , featCols) :
...
Forum: Bioinformatics 02-07-2013, 12:43 AM
Replies: 0
Views: 1,577
Posted By stephenhart
Question mouse GTF

Does anyone know of a mouse gtf that includes cds, tss, and promoters?
Forum: General 12-06-2012, 04:07 AM
Replies: 0
Views: 1,113
Posted By stephenhart
edgeR plotting error

Hello,

I am analyzing count data from RNAseq and, while I can properly run the differential expression analysis, the plotSmear function fails with the warning

" Error in log2(x) :...
Forum: Bioinformatics 02-14-2012, 11:03 PM
Replies: 0
Views: 1,699
Posted By stephenhart
Question Non-species refseq genes in UCSC Genome Browser

Hi,

I am blat-ing sequences using the UCSC Genome Browser to see if the neighboring genes of certain sequences are conserved in different species. There is one track that confuses me: Non-human...
Forum: Bioinformatics 12-14-2011, 06:02 AM
Replies: 0
Views: 1,184
Posted By stephenhart
Identifying chromosomal gene pairs

I have identified, via RNAseq, a number of differentially expressed genes located on the X chromosome. I would like to identify the pairs on the Y chromosome for these genes. Any advice would be...
Forum: General 11-14-2011, 02:33 PM
Replies: 3
Views: 2,522
Posted By stephenhart
Question Comparing mouse and human differentially expressed genes

Hello,

I have run differential expression analyses for mouse and human using RNA-seq data. I now have a list of genes (Ensembl IDs) differentially expressed in the mouse and a list of genes...
Forum: General 11-08-2011, 03:55 AM
Replies: 5
Views: 3,809
Posted By stephenhart
Got it working now. Thanks for your help.

Got it working now. Thanks for your help.
Forum: General 11-07-2011, 11:12 AM
Replies: 5
Views: 3,809
Posted By stephenhart
Excuse my ignorance. How do I apply as.integer to...

Excuse my ignorance. How do I apply as.integer to my columns?
Forum: General 11-07-2011, 10:07 AM
Replies: 5
Views: 3,809
Posted By stephenhart
Question error in DESeq analysis

Hello,

I have RNA-seq data, which I am trying to analyze with DESeq. My file (.csv) appears to be correct

>head(myfile)
"
gene_id VZ_w13 VZ_w14a VZ_w14b VZ_w15a VZ_w15b VZ_w16a
1...
Forum: Bioinformatics 10-11-2011, 01:45 AM
Replies: 0
Views: 1,209
Posted By stephenhart
comparative genomics with a human pseudogene

I have identified a pseudogene in my human RNA-seq data. I would like to know how well this gene is conserved in (i) other primates and (ii) other mammals. Is the best course of action to put the...
Forum: Bioinformatics 09-28-2011, 10:18 AM
Replies: 2
Views: 2,948
Posted By stephenhart
Question long ncRNA from RNA-seq

I am a biologist and a poor programmer. I have assembled RNA-seq data from which I'd like to extract all potential long ncRNA candidates. I assume the easiest way would be to compare my data to...
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