Processing RNA-seq data by following Roadmap Epigenomics Pipeline
Is there anybody who followed the RNA-seq data analysis pipeline used for processing data used in Epigenomics Roadmap publication? If yes, kindly share your experience.
roadmap
rna-seq
• 1,973 views
•
link
written
by
Bioinformatist Newbie
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Merging replicates from Encode/Roadmap project
written by curious •Hi, I'm processing data from the [Encode project][1] to look at the enhancer-promoter interactions. I would like to merge the replicates (technical/biological) for a given …
-
Data resources for Chromatin accessibility (DNAse, FAIRE, ATAC - seq) and Transcriptomics (RNA-seq,…
written by Bioinformatist NewbieI know following resources which have DNAse-seq and mRNA-seq data for different tissue/cell samples. If you know some other studies or resources, then kindly share …
-
Polyadenylation cleavage sites detection from rRNA-depleted RNA-Seq
written by Nicolas Rosewick<p>Hi,</p> <p>I try to detect specific polyadenylation cleavage site in my RNA-Seq data. Anyone has tried that using rRNA-depleted RNA-Seq (2x100bp). Is there sufficient polyA …
-
Binning -log10 P signal tracks
written by Saulius LukauskasI am looking at the recently published signal tracks from Roadmap Epigenomics project. Namely the section d in http://egg2.wustl.edu/roadmap/web_portal/processed_data.html. They suggest using their -log10 p-value …
-
Can Trinity (de novo) be coupled to Tophat?
written by GPRHello, I understand that Trinity data can be post-processed with Bowtie and later with RSEM. [*Nature protocols* 8.8 (2013): 1494-1512][1]. I would like to know …
-
Which Genome Synteny Program?
written by jomaco<p>Hi,</p> <p>I'm interested in producing an image similar to figure 1 in this paper: <a href='http://www.nature.com/nature/journal/v461/n7262/full/nature08358.html#a2'>http://www.nature.com/nature/journal/v461/n7262/full/nature08358.html#a2</a></p> <p>Can anyone identify the program which may have been …
-
Tutorial: Rna-Seq Review Papers
written by Istvan Albert## Review papers on the topic of RNA-seq ### General Guides - [Computational methods for transcriptome annotation and quantification using RNA-seq (May 2011)][1] in Nature …
-
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
written by Istvan AlbertThis protocol describes in detail how to use TopHat and Cufflinks to perform RNA-seq analyses. It also covers several accessory tools and utilities that aid …
-
Datasets For Which There Is Microarray And Rna-Seq Data On The Same Samples
written by Paul<p>Hi,</p> <p>I'm wondering if anyone is aware of datasets for which there is publicly available microarray and RNA-seq data on the same samples?</p> <p>So far …
-
How Are Storage Requirements Affected By The New Ion Torrent Sequencing Technology?
written by Samuel Lampa<p>A <a href="http://www.nature.com/nature/journal/v475/n7356/full/nature10242.html">publication about the new Ion Torrent tech</a> was published the other day on Nature.</p> <p>... but they mention nothing on produced data amounts. …