So, enter 20 in the minimum quality text box. The generally considered minimum quality to keep a base is 20.We need to cut off at the end of the reads, therefore, we will select ‘Cut bases off the ens of a read, if below a threshold quality (TRAILING)’. Now, select for the R1 input file, select output file from the last step, namely ‘FASTQ de-interlaced left mates from data2‘ fand then for the R2 input file, select another output file, namely, ‘ FASTQ de-interlaced right mates from data2‘ from the next dropdown menu.Select ‘Paired-end (two separate input files)’ from the dropdown.This will create four different files: one file for forward reads, one for reverse reads, and reads without a pair are placed into the other two files.Īfter deinterlacing our file, we will perform trailing on our two first output files. Select fastq dataset, i.e., your interleaved file containing paired-end reads.Click on the ‘FASTQ de-interlacer’ in the GALAXY tools. Since this file is interleaved, we will have to deinterlace it.We have an interleaved file of paired-end reads, let’s call it ‘input.fastq’. Trailing means cutting off the reads from the 3′-end (i.e., from right to left). In this article, we are going to perform trailing on NGS paired-end reads data using the GALAXY platform. These functions include trailing, leading, and several other quality control operations. It is a flexible tool providing several functions to be operated on reads. Trimmomatic is a read trimming tool for Illumina NGS data.
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