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A new book has come out on RNA-seq data analysis and it is written by none other than our long time reader Mikael Huss, along with four other authors. You can get the book at the publisher’s website through following link.
RNA-seq Data Analysis: A Practical Approach (By: [...]
Posted on 29 September 2014 | 7:58 am
At last we get the analysis of Oxford Nanopore data that we had been looking for since first day. Michael Schatz posted the GI2014 slides of James Gurtowski from his lab in his website.
—————————– Read Length Distribution
Read length goes all the way to ~147Kb, but the longer reads are problematic (see next section).[...]
Posted on 26 September 2014 | 8:51 am
About two years back, we reported about Succinct de Bruijn Graph construction by Alex Bowe and collaborators. Also, earlier this year, HKU group of professor Tak-Wah Lam published their implementation of GPU-Accelerated BWT Construction for Large Collection of Short Reads. Now those two are combined along with ideas from IDBA-UD into a metagenome assembler. The [...]
Posted on 25 September 2014 | 8:03 pm
RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput short-read sequencing of cDNA. However, as ongoing advances are rapidly yielding increasing read lengths, a technical hurdle remains in identifying the degree to which differences in [...]
Posted on 25 September 2014 | 11:01 am
We came across this BMC Genomics paper in twitter, but did not get time to read yet. Hopefully, the readers will find it useful.
Background Gene expression analysis by RNA sequencing is now widely used in a number of applications surveying the whole transcriptomes of cells and tissues. The recent introduction of ribosomal RNA [...]
Posted on 12 August 2014 | 9:49 am
In the past, we talked about ‘short read noise’, which is the noise introduced by clean short reads due to being short. Readers may take at these two of our earlier commentaries for details.
End of Short-Read Era? – (Part I)
End of Short-Read Era? – (Part II)
An excellent biorxiv paper analyzing RNA-seq assemblies [...]
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We came across this cool paper from 2013.
Next-generation sequencing has become an essential tool in molecular biology that has been successfully applied to a broad variety of experimental approaches. While several platforms for next-generation sequencing exist, the most commonly used approach is sequencing-by-synthesis, implemented on Illumina’s Genome Analyzer II (GAII) and HiSeq2000 systems. A [...]
Posted on 16 September 2014 | 7:14 am
Next Generation Sequencing (NGS) technology is based on cutting DNA into small fragments, and their massive parallel sequencing. The multiple overlapping segments termed “reads” are assembled into a contiguous sequence. To reduce sequencing errors, every genome region should be sequenced several dozen times. This sequencing approach is based on the assumption that genomic DNA [...]
Posted on 10 June 2014 | 6:08 am
We had been pondering about those cryptic terms and found by asking some people around that the P stands for polymerase and C stands for chemistry. Therefore, P4-C2 means polymerase of fourth generation and chemistry of second generation.
That got us curious about what the actual DNA polymerase sequences are for 2nd, 3rd or [...]
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