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Forum: Bioinformatics 07-05-2015, 02:53 PM
Replies: 6
Views: 1,427
Posted By bjackson
I do primarily single ended reads, but for...

I do primarily single ended reads, but for alignment quality I look primarily at
1) pct of reads mapped
2) pct of reads uniquely mapped

It sounds like you are also asking about post-alignment qc...
Forum: Bioinformatics 07-05-2015, 02:48 PM
Replies: 5
Views: 3,797
Posted By bjackson
I just ended up asking a very similar question...

I just ended up asking a very similar question looking for guidance. When you say 'widely recommended' can you provided a paper or technical reference that says this? That would help me greatly.
Forum: Bioinformatics 07-05-2015, 02:43 PM
Replies: 2
Views: 3,036
Posted By bjackson
Question about biological vs technical replicates in RNA-seq analysis

Generally when I receive RNA seq data, I get biological and technical replicates. IE if there are two conditions (eg treated vs untreated), there will be three samples Treated-A, Treated-B,...
Forum: Bioinformatics 05-12-2015, 09:09 AM
Replies: 1
Views: 806
Posted By bjackson
Still looking through this data set. I have 194...

Still looking through this data set. I have 194 named differentially expressed genes. What is the 'normal' amount of differentially expressed genes that you would expect? I know it can vary a lot...
Forum: Bioinformatics 05-11-2015, 05:36 PM
Replies: 1
Views: 806
Posted By bjackson
CummeRbund shows 95% NAs for gene name lists

cuff_data = readCufflinks(dir=paste0(getwd(),"/../cuffdiff/"),
gtfFile = paste0(getwd(),"/../cuffmerge/merged.gtf"),
genome="hg19", rebuild=F)...
Forum: Bioinformatics 05-08-2015, 09:37 AM
Replies: 0
Views: 2,321
Posted By bjackson
Normalization and analysis of proteomic spectral count data

I have spectral count data (SomaScan proteomics read).

What I have is protein name / uniprot identifier and a count (e.g., 188.9 or 106219.5).

I wanted to use PLGEM in R / bioconductor to...
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