(B ) Intronic reads of poly(A )- RNA-seq form a gradient as a consequence of co-transcriptional splicing and elongation rates.
Therefore, we downloaded lung and kidney RNA-seq data form bodymap project [ 20].
The expression data were obtained as processed RNA-seq data in the form of RNA-seq by Expectation Maximization (RSEM) [ 22].
Genomic regions mapped by specific histone modifications may fail to be sequenced by ChIP-seq or to form peaks, in which case they would be overlooked by peak calling tools.
This technology based on the relatively short sequenced reads (data form RNA-seq and Tag-seq) also had its drawbacks, especially for the organisms without reference genome sequence.
We define a weighted splice-graph representation of RNA-seq data, summarizing in compact form the alignment of RNA-seq reads to a reference genome.
Originally designed for the analysis of microarray data, it has been extended to the analysis of RNA-seq data in the form of normalized log2-transformed counts.
Reduced to its current, simplest form, TCR-seq involves PCR amplification and sequencing of the CDR3 region from one of the TCR subunits.
ChIP-Seq experiments not only form the backbone of several large international research initiatives (Adams et al, 2012; Dunham et al, 2012), but also represent a powerful tool for individual research laboratories.
We would like to thank N. Chen for help with extracting data from Wormbase, D. Napier for help with hosting the local GExplore database, L. Hillier for providing the stage- and sex-specific RNA-seq data in a form that was easy to process and members of the lab for discussion and comments on the manuscript.
The Potato Genomic Resource (Spud DB) [ 25] also provides potato RNA-seq data in the form of raw short read sequence files and of FPKM normalized results as defined by the Cufflinks pipeline [ 26] (analogous to the RPKM normalization [ 27]) in Excel format, as well as visualization of expression tracks by library in a potato genome browser.
