ABMapper
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Application data |
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| Created by | Shaoke Lau |
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| Biological application domain(s) | Genomics, Transcriptomics |
| Principal bioinformatics method(s) | Read mapping, Sequence alignment |
| Technology | Illumina |
| Created at | The Chinese University of Hong Kong |
| Maintained? | Yes |
| Input format(s) | SAM |
| Output format(s) | SAM, BED |
| Programming language(s) | C++, Perl |
| Licence | GPLv3 |
| Operating system(s) | Linux |
Summary: Maps RNA-Seq reads to target genome considering possible multiple mapping locations and splice junctions
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Description
Sequencing reads generated by RNA-sequencing (RNA-seq) must first be mapped back to the genome through alignment before they can be further analyzed. Current fast and memory-saving short-read mappers could give us a quick view of the transcriptome. However, they are not designed for reads that span across splice junctions, nor for repetitive reads, which can be mapped to multiple locations in the genome (multi-reads). Here we describe a new software package: ABMapper, which is specifically designed for exploring all putative locations of reads that are mapped to splice junctions or repetitive in nature. Availability and Implementation: The software is freely available at: http://abmapper.sourceforge.net/. The software is written in C++ and PERL. It runs on all major platforms and operating systems including Windows, Mac OS X and LINUX
Links
References
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| Web Search | Wiki Sites | Scientific |
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