When, in early 2013, we covered Eran Elhaik’s paper on the origin of European Jewish population, he was treated everywhere like a pariah. Haldane’s Sieve blog, which supposedly posts all interesting pop-gen preprints from arxiv, completely ignored his paper. Yet, as it turned out over the last 18 months, Elhaik’s paper became the second most [...]
Posted on 10 September 2014 | 10:02 pm
T. Ryan Gregory, who had been fighting ENCODE’s junk science since 2007, is fed up with another high-profile paper published in Nature. He wrote in Twitter –
The paper in question has over seventy authors, which tends to scare us these days. More authors mean higher chance of ‘faddish stuff’ or ‘fashionable ideas’ [...]
Posted on 10 September 2014 | 8:35 pm
Nick Loman uploaded his E. coli nanopore data on GigaDB.
Here we present a read dataset from whole-genome shotgun sequencing of the model organism Escherichia coli K-12 substr. MG1655 generated on a MinION device with R7 chemistry during the early-access MinION Access Program (MAP).
Three sequencing runs of the MinION were performed using R7 chemistry. [...]
Posted on 10 September 2014 | 1:20 pm
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 [...]
Posted on 16 July 2014 | 3:14 am
Richard Smith-Una, whose work was covered in our blog, releases a new quality assessment program (transrate) that we surely like to check out.
Transcriptome assembly is hard. The algorithms are complex, the data are messy, and it’s often not clear how to determine whether an assembly is suitable for answering a biological question.
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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 [...]
Posted on 4 April 2014 | 4:58 am
Changing genome in plants used to be incredibly difficult, but not any more. Here is an excellent review –
Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system
Targeted genome engineering (also known as genome editing) has emerged as an alternative to classical plant breeding and transgenic (GMO) [...]
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