| Chapter title |
Visitor, an informatic pipeline for analysis of viral siRNA sequencing datasets.
|
|---|---|
| Chapter number | 7 |
| Book title |
Antiviral RNAi
|
| Published in |
Methods in molecular biology, March 2011
|
| DOI | 10.1007/978-1-61779-037-9_7 |
| Pubmed ID | |
| Book ISBNs |
978-1-61779-036-2, 978-1-61779-037-9
|
| Authors |
Antoniewski C, Christophe Antoniewski, Antoniewski, Christophe |
| Abstract |
High-throughput sequencing emerged as a powerful approach to characterize siRNA populations -generated by hosts in response to viral infections. Here we described an informatic pipeline visitor to analyze in-house large sequencing datasets generated from Illumina sequencing of Drosophila small RNA libraries. The visitor perl script is designed to treat fastq sequence datasets from the Illumina sequencing platform, using a computer running under a UNIX compliant operating system (MacOS X, Linux, etc.). visitor first generates a detailed report of the sequence quality of the Illumina run. Then, using the Novoalign software, the script removes reads that match with the D. melanogaster genome from the sequencing data set. The remaining reads are aligned to a viral reference library, which can contain one or several virus genomes. visitor provides a hit table of identified viral siRNAs as well as graphics eps files of viral siRNA profiles. Unmatched small RNAs are also available in a fast format for de novo assembly and new virus discovery. |
Mendeley readers
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 19 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Bachelor | 3 | 16% |
| Researcher | 3 | 16% |
| Other | 2 | 11% |
| Professor > Associate Professor | 2 | 11% |
| Student > Master | 2 | 11% |
| Other | 2 | 11% |
| Unknown | 5 | 26% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 5 | 26% |
| Agricultural and Biological Sciences | 5 | 26% |
| Social Sciences | 1 | 5% |
| Medicine and Dentistry | 1 | 5% |
| Engineering | 1 | 5% |
| Other | 0 | 0% |
| Unknown | 6 | 32% |