ALFA: Annotation landscape for aligned readsNGS, Quality control, Post mapping, Universal, ToolBackground The last 10 years have seen the rise of countless functional genomics studies based on Next-Generation Sequencing (NGS). In the vast majority of cases, whatever the species, whatever the......
ALFA provides a global overview of features distribution composing NGS dataset(s). Given a set of aligned reads (BAM files) and an annotation file (GTF format with biotypes), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, ...
Mapping short DNA sequencing reads and calling variants using mapping quality scores Here we introduce the concept of mapping quality, a measure of the confidence that a read actually comes from the position it is aligned to by the ...
RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the w
Import reads from an Amplicon Variant Analyzer projectChristoph Bartenhagen
Total number of uniquely aligned reads.Philip MöllerAaron OverlöperKonrad U. FörstnerTuanNan WenCynthia M. SharmaErhMin LaiFranz Narberhaus
We developed a Bayesian mixture model called SNVmix for this purpose that takes as input the complete set of aligned reads and produces as output the probability of an SNV at each position represented in the data.Sohrab P. ShahRyan D. Morin...
Table S1 . List of ChIP-Seq datasets showing numbers of aligned reads .Ku, ManchingKoche, Richard PRheinbay, EstherMendenhall, Eric MEndoh, MitsuhiroMikkelsen, Tarjei SPresser, AvivaNusbaum, ChadXie, XiaohuiChi, Andrew S
Correspondence between BioAnalyzer traces and the length distribution of aligned reads.Michael BaymSergey KryazhimskiyTami D. LiebermanHattie ChungMichael M. DesaiRoy Kishony
Alu elements constitute a notable part of the human genome and greatly affect processes related to maintenance of genome integrity. One of the basic methods for studying variation in the genome, including Alu elements, is genome sequencing followed by mapping the reads to a reference genome ...