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Forum: RNA Sequencing 03-21-2016, 07:10 PM
Replies: 1
Views: 1,275
Posted By Sentinel156
DGE using stranded and unstranded Illumina libraries

Hi all,

I am working with S. pombe doing 100bp single end Illumina HiSeq 2500 RNA-seq. Despite being told the trueseq stranded protocol was used one lot of my libraries appear unstranded (roughly...
Forum: RNA Sequencing 06-09-2015, 05:29 PM
Replies: 2
Views: 1,711
Posted By Sentinel156
Thanks for the reply Michael, After looking...

Thanks for the reply Michael,

After looking over a PCA plot containing all of my replicates the glycerol condition replicates do not clearly cluster independently of the other conditions. It is...
Forum: RNA Sequencing 06-07-2015, 09:26 PM
Replies: 2
Views: 1,711
Posted By Sentinel156
DESeq2 workflow problem

Hi everyone,

I'm investigating differentially expressed genes in my wild-type yeast vs a mutant strain. Each strain has been cultured in three different conditions (glucose, sucrose, glycerol)....
Forum: RNA Sequencing 05-19-2015, 12:19 AM
Replies: 1
Views: 1,480
Posted By Sentinel156
Tophat2 output bam size discrepancies

Hi all,

I'm seeing tophat2 output bam files of different sizes (~800mb vs ~300mb) for two fastq files from the same strain (different biological replicates) with similar total read numbers for...
Forum: RNA Sequencing 10-08-2014, 05:39 PM
Replies: 0
Views: 1,556
Posted By Sentinel156
cuffmerge samples from different strains or leave separate

Hi,

Possibly a naive question but I am new to RNA-seq analysis. I have RNA-seq (illumina hi-seq 100bp single end) samples from four different yeast strains (one WT, one deletion mutant and the...
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