comparison rmarkdown_samtools_flagstat.Rmd @ 5:1c16536c70f5 draft

update

4:ec39bfeaf496

  error = TRUE
)
```


# Reads alignment stats

```{r 'flagstat'}
command = paste0('samtools flagstat ', opt$input_bam, ' > ', paste0(opt$report_dir, '/report.txt'))
system(command)
df = readLines(paste0(opt$report_dir, '/report.txt')) %>%

5:1c16536c70f5

  error = TRUE
)
```


# Reads alignment stats on `r opt$input_bam_name`

```{r 'flagstat'}
command = paste0('samtools flagstat ', opt$input_bam, ' > ', paste0(opt$report_dir, '/report.txt'))
system(command)
df = readLines(paste0(opt$report_dir, '/report.txt')) %>%