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Forum: RNA Sequencing

06-18-2014, 07:47 AM

Replies: 33

Error: gtf_to_fasta returned an error.

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

Additonal replicates for RNA-seq from separate HiSeq run

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

exon and intron numbers of genes

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

Removing overlapping genes from annotation for RNAseq read count

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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