Forum: Bioinformatics
05-03-2013, 12:24 AM
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Replies: 0
Views: 1,003
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Forum: Bioinformatics
04-30-2013, 06:08 AM
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Replies: 0
Views: 1,194
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.
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Forum: Bioinformatics
04-30-2013, 05:06 AM
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Replies: 1
Views: 2,695
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...
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Forum: Bioinformatics
03-15-2013, 07:16 AM
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Replies: 2
Views: 2,924
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Forum: Bioinformatics
02-24-2013, 01:35 AM
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Replies: 1
Views: 1,979
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....
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Forum: Bioinformatics
02-08-2013, 08:13 AM
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Replies: 3
Views: 3,199
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) :
...
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Forum: Bioinformatics
02-07-2013, 12:43 AM
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Replies: 0
Views: 1,577
mouse GTF
Does anyone know of a mouse gtf that includes cds, tss, and promoters?
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Forum: General
12-06-2012, 04:07 AM
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Replies: 0
Views: 1,113
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) :...
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Forum: Bioinformatics
02-14-2012, 11:03 PM
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Replies: 0
Views: 1,699
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...
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Forum: Bioinformatics
12-14-2011, 06:02 AM
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Replies: 0
Views: 1,184
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...
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Forum: General
11-14-2011, 02:33 PM
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Replies: 3
Views: 2,522
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Forum: General
11-08-2011, 03:55 AM
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Replies: 5
Views: 3,809
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Forum: General
11-07-2011, 11:12 AM
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Replies: 5
Views: 3,809
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Forum: General
11-07-2011, 10:07 AM
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Replies: 5
Views: 3,809
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...
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Forum: Bioinformatics
10-11-2011, 01:45 AM
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Replies: 0
Views: 1,209
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...
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Forum: Bioinformatics
09-28-2011, 10:18 AM
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Replies: 2
Views: 2,948
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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