Selected article for: "low quality and minimum length"
Author: Nelly Mostajo Berrospi; Marie Lataretu; Sebastian Krautwurst; Florian Mock; Daniel Desirò; Kevin Lamkiewicz; Maximilian Collatz; Andreas Schoen; Friedemann Weber; Manja Marz; Martin Hölzer
Title: A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
  • Document date: 2019_8_19
    • ID: ihqvcxv6_14
    Snippet: To validate our novel ncRNA predictions, we selected six RNA-Seq data sets 16, 33, [36] [37] [38] comprising alltogether 98 samples gathered from four different bat species. We have labeled each published RNA-Seq data set based on the first authors last name and the year of data set publication (Tab. 2 and Tab. S2). All samples were quality trimmed using Trimmomatic 39 (v0.36) with a 4 nt-step slidingwindow approach (Q20) and a minimum remaining .....
    Document: To validate our novel ncRNA predictions, we selected six RNA-Seq data sets 16, 33, [36] [37] [38] comprising alltogether 98 samples gathered from four different bat species. We have labeled each published RNA-Seq data set based on the first authors last name and the year of data set publication (Tab. 2 and Tab. S2). All samples were quality trimmed using Trimmomatic 39 (v0.36) with a 4 nt-step slidingwindow approach (Q20) and a minimum remaining read length of 20 nt. For the Field-2018 data set 38 we additionally removed the three leading 5' nucleotides from the reads of each sample because of a generally low quality observed by FastQC (www.bioinformatics. babraham.ac.uk/projects/fastqc/) (v0.11.7). The remaining reads of all processed samples were individually mapped to all 16 bat assemblies using HISAT2 34 (v2.1.0) and transcript abundances were subsequently calculated from all resulting 1,568 mappings by featureCounts 35 (v1.6.3).

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