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Forum: RNA Sequencing 06-18-2014, 07:47 AM
Replies: 33
Views: 7,870
Posted By DRAT
Hi hathiram2, I recently had the same...

Hi hathiram2,

I recently had the same problem after downloading mm10 sequences/annotation files from the tophat website. Check the content of the genome.fa file because for me it was empty and I...
Forum: Bioinformatics 11-29-2012, 04:12 AM
Replies: 1
Views: 1,138
Posted By DRAT
Additonal replicates for RNA-seq from separate HiSeq run

Hello,

We are planning to generate additional replicates for RNA-seq experiment and I would like to ask for opinions on the experimental design and make sure that our approach is valid.

We...
Forum: Bioinformatics 11-07-2012, 02:06 PM
Replies: 2
Views: 1,817
Posted By DRAT
Hello Rama, PeakAnalyzer will do it for you....

Hello Rama,

PeakAnalyzer will do it for you. If you work with human or mouse genome the annotation is also provided within the program.
...
Forum: Bioinformatics 11-06-2012, 08:28 AM
Replies: 2
Views: 2,486
Posted By DRAT
Removing overlapping genes from annotation for RNAseq read count

Hello,

I am trying to prepare a read count table for DESeq using EasyRNAseq package in R. I followed the vignette and used ensembl.gtf file as my annotation. After constructing my read count table...
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