CCRRBL-19/RBL-19.rmd at main · NCI-RBL/CCRRBL-19 · GitHub

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---
title: "RBL-19"
author: "Wilfried Guiblet"
output:
  github_document:
    html_preview: true
date: "`r Sys.Date()`"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, warning = FALSE, message = FALSE)
setwd("/Users/guibletwm/Lab_Work/CCRRBL-15")
library(ggplot2)
library(dplyr)
library(ggpubr)
library(rstatix)
```

# Tailer Analysis

```{bash, eval=FALSE}
module load python
#pip install jla-tailer
Tailer -a references/gencode.v49.annotation.gtf rawfiles/17.bam
Tailer -a references/gencode.v49.annotation.gtf rawfiles/17multi.bam
Tailer -a references/gencode.v49.annotation.gtf rawfiles/99.bam
Tailer -a references/gencode.v49.annotation.gtf rawfiles/99multi.bam
Tailer -a references/gencode.v49.annotation.gtf rawfiles/ctrl.bam
Tailer -a references/gencode.v49.annotation.gtf rawfiles/c_multi.bam

mv rawfiles/*_tail.csv Tailer/gencode_genes/
```


export NXF_SINGULARITY_CACHEDIR=$PWD/.singularity
export SINGULARITY_CACHEDIR=$PWD/.singularity

singularity pull bed2gtf.sif docker://wilfriedguiblet/bed2gtf:v0.1
singularity shell -B $(pwd)/:/data2/ bed2gtf.sif

bed2gtf -b hg38-tRNAs.bed -o hg38-tRNAs.gtf --no-gene

# Appends gene_name "<gene_id_value>" at the end of the line:
sed -E 's/(gene_id "([^"]+)";)/\1 gene_name "\2"/' hg38-tRNAs.gtf > hg38-tRNAs.withnames.gtf


# switch to exon
vim /home/guibletwm/.local/lib/python3.10/site-packages/Tailer/TailerFunctions.py


```{bash, eval=FALSE}
module load python
#pip install jla-tailer
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/17.bam
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/17multi.bam
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/99.bam
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/99multi.bam
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/ctrl.bam
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/c_multi.bam


#c_multi is too big

samtools view -s 0.25 -b rawfiles/c_multi.bam > rawfiles/c_multi.subset.bam
samtools index rawfiles/c_multi.subset.bam
Tailer -a references/hg38-tRNAs.withnames.gtf rawfiles/c_multi.subset.bam
mv rawfiles/c_multi.subset_tail.csv Tailer/tRNAs/


```