Round 5 PickSeq (F9 and F12).ipynb

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    "**Rename Files by removing the first 23 characters**\n",
    "\n",
    "```\n",
    "for file in *; do mv $file `echo $file | cut -c23-`; done\n",
    "```\n",
    "\n",
    "**Unzip all the files**\n",
    "```\n",
    "bunzip2 *.bz2\n",
    "```\n",
    "\n",
    "**Create the alignment.csv file**\n",
    "\n",
    "```\n",
    "(echo 'samplename,description'; for f in raw/*fastq; do readlink -f $f | perl -pe 's/(.*?_(S[0-9]+)_.*)/\\1,\\2/'; done) > alignment.csv\n",
    "```\n",
    "\n",
    "**Merge multiple files into a single file**\n",
    "\n",
    "```\n",
    "#!/bin/sh\n",
    "#SBATCH -p priority\n",
    "#SBATCH -J merge\n",
    "#SBATCH -o run.o\n",
    "#SBATCH -e run.e\n",
    "#SBATCH -t 0-12:00\n",
    "#SBATCH --cpus-per-task=20\n",
    "#SBATCH --mail-type=END         # Type of email notification- BEGIN,END,FAIL,ALL\n",
    "#SBATCH --mail-user=ajitj_nirmal@dfci.harvard.edu   # Email to which notifications will be sent\n",
    "\n",
    "module load bcbio/latest\n",
    "cd raw\n",
    "bcbio_prepare_samples.py --memory-per-job 2G --out merged --csv tomerge.csv \n",
    "```\n",
    "\n",
    "**Download the reference genome**\n",
    "\n",
    "```\n",
    "mkdir reference\n",
    "cd reference\n",
    "wget ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz\n",
    "wget ftp://ftp.ensembl.org/pub/release-96/gtf/homo_sapiens/Homo_sapiens.GRCh38.96.gtf.gz\n",
    "gunzip *\n",
    "```\n",
    "\n",
    "**Create the alignment.csv file**\n",
    "\n",
    "```\n",
    "(echo 'samplename,description'; for f in merged/*fastq.gz; do readlink -f $f | perl -pe 's/(.*?_(S[0-9]+)_.*)/\\1,\\2/'; done) > alignment.csv\n",
    "```\n",
    "\n",
    "**Prepare the O2.yaml file**\n",
    "\n",
    "```\n",
    "cd ..\n",
    "vim O2.yaml\n",
    "\n",
    "details:\n",
    "  - analysis: RNA-seq\n",
    "    genome_build: hg38\n",
    "    algorithm:\n",
    "      transcriptome_fasta: /n/scratch3/users/a/ajn16/f12/reference/Homo_sapiens.GRCh38.cdna.all.fa\n",
    "      transcriptome_gtf: /n/scratch3/users/a/ajn16/f12/reference/Homo_sapiens.GRCh38.96.gtf\n",
    "      aligner: hisat2\n",
    "      strandedness: unstranded\n",
    "      tools_on: [bcbiornaseq]\n",
    "      bcbiornaseq:\n",
    "          organism: homo sapiens\n",
    "upload:\n",
    "  dir: ../final\n",
    "```\n",
    "\n",
    "**Intiate bcBio**\n",
    "\n",
    "```\n",
    "module load bcbio/latest\n",
    "unset PYTHONPATH\n",
    "bcbio_nextgen.py -w template O2.yaml alignment.csv merged/\n",
    "```\n",
    "\n",
    "**Create Submission script to O2**\n",
    "\n",
    "```\n",
    "vim submit_bcbio.sh\n",
    "\n",
    "#!/bin/sh\n",
    "#SBATCH -p priority\n",
    "#SBATCH -J pickseq\n",
    "#SBATCH -o run.o\n",
    "#SBATCH -e run.e\n",
    "#SBATCH -t 10-00:00\n",
    "#SBATCH --cpus-per-task=20\n",
    "#SBATCH --mem=150G\n",
    "#SBATCH --mail-type=END         # Type of email notification- BEGIN,END,FAIL,ALL\n",
    "#SBATCH --mail-user=ajitj_nirmal@dfci.harvard.edu   # Email to which notifications will be sent\n",
    "\n",
    "export PATH=/n/app/bcbio/tools/bin:$PATH\n",
    "bcbio_nextgen.py ../config/alignment.yaml \\\n",
    "    -n 24 -t local\n",
    "```\n",
    "\n",
    "\n",
    "**Submit job to O2 for processing**\n",
    "\n",
    "```\n",
    "cp submit_bcbio.sh alignment/work\n",
    "cd alignment/work\n",
    "sbatch submit_bcbio.sh\n",
    "```"
   ]
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