Sentence examples for bases were removed using from inspiring English sources

The unmethylated CpG bases at the 3′ end of the reads were added during end-repair step and therefore, the sequence from the filled-in bases were removed using cleanadaptors (an optional switch (-t) is built into the program to remove these unmethylated filled-in bases).

The remaining reads were quality-trimmed, and adapters and any reads fewer than 40 bases were removed using the FastX toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).edu/fastx_toolkit/

Then, low-quality bases were removed using "Trim sequences" (CLC Genomics Workbench v. 5.5.1; CLC Bio, Aarhus, Denmark), and vector sequences further eliminated.

These 10 bases were removed using the "fastx_trimmer" function from the FASTX-Toolkit [ 29], after which a second FastQC analysis confirmed lack of nucleotide bias along the entire length of reads.

Low quality bases with Phred score <20 corresponding to a probability of error higher than 0.01 [ 33] as well as reads containing unknown bases were removed using FASTQ Quality Filter tool of FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).edu/fastx_toolkit/

Prior to analyzing the data, the quality of raw sequencing reads was checked by the FastQC tool (v0.10.0) [ 51] and low quality and dirty reads with sequence adaptors, more than 20% QA <25 bases or 'N' bases were removed using NGSQCToolkit (v2.3) [ 52].

Sequence reads that contained undetermined bases ("N") were removed using custom-made Perl scripts.

Additionally, the locations of repeat sequences, such as retrotransposons, were obtained [ 29] and reads that overlapped repeat sequences, mitochondrial, or chloroplast locations by at least one base pair were removed using bedtools (v2.19.1) [ 30].

The resulting trimmed reads were checked for contaminants, and low quality bases and contaminants were removed using the cutadapt software (Martin 2011).

Pairwise comparisons were made using Fisher's method at the 95%% significance level.> Illumina adaptor sequences and low quality bases from reads were removed using the software Nesoni (http://www.vicbioinformatics.com/software.nesoni.shtml), using a quality cutoff of 20 and discarding reads shorter than 75 bp.

Poor quality bases at the 3′ end were removed using the tool FASTQ Quality Trimmer (FASTX-Toolkit; fastx-tools_0.0.13_binaries_Linux_2.6_amd64; http://hannonlab.cshl.edu/fastx_toolkit/). Error correction of the remaining reads was done using Coral 1.3 and the standard Linux programs split and cat.