Mercurial > repos > mingchen0919 > rmarkdown_samtools_flagstat
annotate rmarkdown_flagstat.Rmd @ 0:ba913054bbff draft
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| author | mingchen0919 |
|---|---|
| date | Tue, 26 Dec 2017 19:27:41 -0500 |
| parents | |
| children |
| rev | line source |
|---|---|
| 0 | 1 --- |
| 2 title: 'samtools flagstat' | |
| 3 output: | |
| 4 html_document: | |
| 5 number_sections: true | |
| 6 toc: true | |
| 7 theme: cosmo | |
| 8 highlight: tango | |
| 9 --- | |
| 10 | |
| 11 ```{r setup, include=FALSE, warning=FALSE, message=FALSE} | |
| 12 knitr::opts_chunk$set( | |
| 13 echo = ECHO | |
| 14 ) | |
| 15 ``` | |
| 16 | |
| 17 | |
| 18 # Code for computational analysis | |
| 19 | |
| 20 ```{r 'run flagstat'} | |
| 21 command = paste0('samtools flagstat ', opt$input_bam, ' > report.txt') | |
| 22 system(command) | |
| 23 ``` | |
| 24 | |
| 25 |