Deep Fritz 13 Torrent
for the most comprehensive analysis of the solid and ion torrent reads, the reads were aligned to the human genome using the burrows-wheeler aligner (bwa). the alignment with the bwa alignment tool was performed using the default setting for this tool. the bwa alignment tool was used to align the reads to the human genome using the default setting.
deep fritz 13 torrent
after quality and size filtering we evaluated 7,883,393 reads provided by solid and 1,924,046 reads provided by the ion pgm (4.1x difference). both platforms gave good quality reads (average above q30) in the size range of mirnas. the percentage of mirbase mapped and unmapped reads, and sequencing reads removed due to low quality, for both cell lines and platforms is given in figure s1. table 1 shows the number of reads and the set of expressed mirnas determined by mirdeep2 for both cell lines by these two sequencing platforms, including the number of distinct mirnas identified by both platforms for both cell lines, as well platform-specific mirnas.
the bioinformatics pipeline, consisting of the aforementioned software packages, was used to process the solid, ion torrent and illumina rna-seq data. raw reads were filtered by size (18 nt) and quality (q20). the reads were mapped to the human genome assembly (hg19) using the burrows-wheeler aligner (bwa) for solid and ion torrent reads and tophat2 for illumina reads. the tophat2 pipeline uses a splice-aware algorithm, and thus is capable of aligning reads across splice junctions. the mirdeep2 software package, developed at the max-planck-institute of immunobiology and epigenetics, was used to identify mirnas from the filtered reads. figure 2 shows the venn diagram illustrating the number of unique and common mirnas detected by the various sequencing platforms for each cell line.