view htseq_count.Rmd @ 3:1545e24c9ba7 draft

add r-dt

---
title: 'htseq-count analysis'
output: html_document
---

```{r setup, include=FALSE, warning=FALSE, message=FALSE}
knitr::opts_chunk$set(
  echo = as.logical(opt$X_e), 
  error = TRUE
)
```


## Run htseq-count

```{bash}
cd ${X_d}

cat >htseq-count.sh <<EOF
  htseq-count \\
    $(echo ${X_A} | sed 's/,/ /g') \\
    ${X_G} \\
    -f ${X_f} \\
    -r ${X_r} \\
    -s ${X_S} \\
    -a ${X_a} \\
    -t ${X_T} \\
    -i ${X_i} \\
    -m ${X_m} > counts.txt
    
  grep -v '__no_feature\|__ambiguous\|__too_low_aQual\|__not_aligned\|__alignment_not_unique' counts.txt > ${X_c}
EOF
```


```{r}
# display htseq-count job script
htseq_count_sh = paste0(opt$X_d, '/htseq-count.sh')
tags$code(tags$pre(readChar(htseq_count_sh, file.info(htseq_count_sh)$size )))
opt
```

```{bash}
cd ${X_d}
sh htseq-count.sh
```

## Counts

```{r}
count_data = read.table(paste0(opt$X_d, '/counts.txt'), row.names = 1)
sample_names = trimws(strsplit(opt$X_B, ',')[[1]])
colnames(count_data) = rep(sample_names, length = ncol(count_data))
DT::datatable(count_data, caption = "htseq counts for each sample")
```