UMARS: Un-MAppable Reads Solution

Abstract

BackgroundUn-MAppable Reads Solution (UMARS) is a user-friendly web service focusing on retrieving valuable information from sequence reads that cannot be mapped back to reference genomes. Recently, next-generation sequencing (NGS) technology has emerged as a powerful tool for generating high-throughput sequencing data and has been applied to many kinds of biological research. In a typical analysis, adaptor-trimmed NGS reads were first mapped back to reference sequences, including genomes or transcripts. However, a fraction of NGS reads failed to be mapped back to the reference sequences. Such un-mappable reads are usually imputed to sequencing errors and discarded without further consideration.MethodsWe are investigating possible biological relevance and possible sources of un-mappable reads. Therefore, we developed UMARS to scan for virus genomic fragments or exon-exon junctions of novel alternative splicing isoforms from un-mappable reads. For mapping un-mappable reads, we first collected viral genomes and sequences of exon-exon junctions. Then, we constructed UMARS pipeline as an automatic alignment interface.ResultsBy demonstrating the results of two UMARS alignment cases, we show the applicability of UMARS. We first showed that the expected EBV genomic fragments can be detected by UMARS. Second, we also detected exon-exon junctions from un-mappable reads. Further experimental validation also ensured the authenticity of the UMARS pipeline. The UMARS service is freely available to the academic community and can be accessed via http://musk.ibms.sinica.edu.tw/UMARS/.ConclusionsIn this study, we have shown that some un-mappable reads are not caused by sequencing errors. They can originate from viral infection or transcript splicing. Our UMARS pipeline provides another way to examine and recycle the un-mappable reads that are commonly discarded as garbage.

MicroRNA 3' end nucleotide modification patterns and arm selection preference in liver tissues

“…For example, the reads with "0,0" are exactly the same with the reference miRNAs. As reported previously [11,22,23], we also observed that the reference miRNAs from miRBase are not necessary the most abundant ones. The mapping results of all pre-miRNAs in 15 libraries are shown in Additional File 3 (the read counts are not normalized as TPM, transcript per million).…”

“…As described in a previous study [22], the opposite-arm miRNAs are not necessarily kept at lower expression levels than the annotated ones. In this study, the opposite-arm miRNA of hsa-mir-1307 has a higher expression level than the annotated one in most libraries, except for SRX018968 and SRX018971.…”

miRNA arm selection and isomiR distribution in gastric cancer

“…So, the reads with presentation "0,0" are exactly the same with reference miRNAs. Examining the counts of all reads, it is not guaranteed that the reference miRNAs from miRBase are the most abundant ones, which was also observed by other studies [11,12,14]. The mapping result of all pre-miRNAs in G1245N and G1245T library can be accessed in Additional file 2 and 3.…”

Comprehensive analysis of microRNAs in breast cancer

“…After further investigation, more than 85% of the unknown category (data not shown) in the 2 libraries could not be mapped back to the human genome (hg19). Our previous study showed that such unmappable reads could be derived from the exon-exon junctions of novel alternative splicing transcripts or from the transcripts of infection viruses [44]. These unmappable reads warrant further investigation.…”