Herald:The Biostar Herald for Tuesday, July 19, 2022
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The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here.

This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,

Recommendations for clinical interpretation of variants found in non-coding regions of the genome | Genome Medicine | Full Text (genomemedicine.biomedcentral.com)

We convened a panel of nine clinical and research scientists with wide-ranging expertise in clinical variant interpretation, with specific experience in variants within non-coding regions. This panel discussed and refined an initial draft of the guidelines which were then extensively tested and reviewed by external groups.

submitted by: Istvan Albert

140127 rtg vcfeval vcf comparison tool (www.slideshare.net)

A presentation on the challenges of comparing variants.

submitted by: Istvan Albert

GitHub - RealTimeGenomics/rtg-tools: RTG Tools: Utilities for accurate VCF comparison and manipulation (github.com)

RTG Tools is a subset of RTG Core that includes several useful utilities for dealing with VCF files and sequence data. Probably the most interesting is the vcfeval command which performs sophisticated comparison of VCF files.

Conventional tools attempt comparison by directly comparing variant positions, alleles, and genotypes, however they are inherently unable to deal with differences in representation that commonly arise, particularly when dealing with complex variants or when comparing variants produced by different callers.

submitted by: Istvan Albert

Consistent RNA sequencing contamination in GTEx and other data sets | Nature Communications (www.nature.com)

Sample contamination is strongly associated with a sample being sequenced on the same day as a tissue that natively expresses those genes. Discrepant SNPs across four contaminating genes validate the contamination. Low-level contamination affects ~40% of samples and leads to numerous eQTL assignments in inappropriate tissues among these 18 genes. This type of contamination occurs widely, impacting bulk and single cell (scRNA-seq) data set analysis. In conclusion, highly expressed, tissue-enriched genes basally contaminate GTEx and other datasets impacting analyses.

submitted by: Istvan Albert

[1404.1100] A Tutorial on Principal Component Analysis (arxiv.org)

This manuscript focuses on building a solid intuition for how and why principal component analysis works. This manuscript crystallizes this knowledge by deriving from simple intuitions, the mathematics behind PCA. This tutorial does not shy away from explaining the ideas informally, nor does it shy away from the mathematics.

submitted by: Istvan Albert

RATTLE: reference-free reconstruction and quantification of transcriptomes from Nanopore sequencing | Genome Biology | Full Text (genomebiology.biomedcentral.com)

We present RATTLE, a tool to perform reference-free reconstruction and quantification of transcripts using only Nanopore reads. Using simulated data and experimental data from isoform spike-ins, human tissues, and cell lines, we show that RATTLE accurately determines transcript sequences and their abundances, and shows good scalability with the number of transcripts.

submitted by: Istvan Albert

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