The peer review process is broken. Once an article is published, there is no means of bringing corrections to the published article. There is no mechanism to correct any error detected in a published article. Neither the corresponding author, nor the editor, will generally respond to emails pointing out problems in published articles. In 2016, every published article should at least have a comments section where the content of the article can be debated.
In frustration at the lack of any means to point out errors in published articles, I have started this thread to point out egregious errors in published articles. Inevitably, I will be asked to reproduce the results of the single article that used an incorrect analysis method, since this will be the article that got the desired results.
I'll admit that I myself do occasionally make errors, including perhaps in my interpretation of the articles below, but there really has to be some mechanism to point out mistakes in published papers. At the very least, there should be a forum where controversial points can be debated.
Article: "MicroRNA and mRNA Cargo of Extracellular Vesicles from Porcine Adipose Tissue-Derived Mesenchymal Stem Cells"
In the article cited, Erin et al. claim to have “comprehensively characterized the mRNA and miRNA expression profile of EVs derived from porcine adipose tissue-MSCs”. Yet, they prepared their library using “poly-A mRNA, purified from total RNA using oligo dT magnetic beads”. So, only poly-adenylated RNAs with a length of at least 50 bases should be present in their libraries. No mature miRNAs should be present.
The programs they use in their analysis, CAP-miRSeq and mirDeep2, were designed specifically for small RNA-Seq libraries. Erin et al. do not mention anywhere in their article any adaptation they brought to the programs to run them on long RNA-Seq libraries. I don’t see how a comprehensive miRNA analysis can be performed with MirDeep2 on a long RNA-Seq library, without any short RNAs.
Also, I cannot find a link to the raw or processed data, which should really be obligatory to provide with any NGS study.
Article: "Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs."
"Sequence analysis of long RNA reads 100nt paired-end reads from 8 samples (4 Sham, 4 LAD) were mapped to mm9 reference genome using Tophat software version 2.0.5 (Trapnell et al., 2012) with option “Gene model” -G, using mm9 UCSC reference genes GTF (Karolchik et al., 2003). An ab initio transcript reconstruction was performed using Cufflinks, version 2.0.2 (Trapnell et al., 2012). The option “masking” (–G) was used, using mm9 UCSC reference genes GTF. The other parameters were default. The resulting GTFs were merged using Cuffmerge, version 2.0.2 (Roberts et al., 2011), using option –g with mm9 UCSC GTF as reference, allowing distinguishing known and novel transcripts."
WTF?? The Cufflinks option -G is for masking? Am I making a mistake in my comprehension of how Cufflinks works?