RNASeq tutorial for Tayla and Mark

Processing RNASeq data
@author: Ajit Johnson Nirmal
Created on Tue Jan 19 12:03:47 2021

#### Move all the files fom inside a folder to outside and remove empty folders

```
find . -name '*.fq.gz' -exec mv {} . \;
find . -name '*.txt' -exec rm {} \;
find . -depth -type d -empty -exec rmdir {} \;
```

####  Create a sample description file and edit to include metadata regarding the samples

```
(echo 'samplename'; for f in raw/*; do readlink -f $f ; done) > alignment.csv
```

#### Prepare the O2.yaml file

```
details:
  - analysis: RNA-seq
    genome_build: hg38
    algorithm:
      aligner: hisat2
      strandedness: unstranded
upload:
  dir: ../final
```

#### Intiate bcBio
```
module load bcbio/latest
bcbio_nextgen.py -w template O2.yaml alignment.csv raw/
```

#### Create Submission script to O2

```
#!/bin/sh
#SBATCH -p priority
#SBATCH -J RNASeq
#SBATCH -o run.o
#SBATCH -e run.e
#SBATCH -t 2-00:00
#SBATCH --cpus-per-task=20
#SBATCH --mem=150G
#SBATCH --mail-type=END         
#SBATCH --mail-user=ajitj_nirmal@dfci.harvard.edu 

export PATH=/n/app/bcbio/tools/bin:$PATH
bcbio_nextgen.py ../config/alignment.yaml \
    -n 24 -t local
```

#### Submit job to O2 for processing

```
cp submit_bcbio.sh alignment/work
cd alignment/work
sbatch submit_bcbio.sh
```