Skip to content

bowtie_alignment_pipeline

Jump to bottom
quantumdot edited this page Jun 8, 2017 · 1 revision

Prerequisites

Installed Packages

This pipeline requires a number of third-party packages for various QC and core pipeline steps. Please ensure that the following are installed:

  • Trimmomatic - used if --trim is passed
  • fastqc - used if --qc fastqc is passed
  • fastq_screen - used if --qc fqscreen is passed
  • bowtie - version 1 or 2, depending on the argument passed to --bowtie-version
  • samtools - required to convert sam to bam from bowtie output, required by PBC analysis
  • picard-tools - required for PBC analysis (--qc pbc) and insert-size metrics (--qc ism)
  • bedtools - required for PBC analysis (--qc pbc)
  • deeptools - required for generation of RPKM-normalized bigwig files (--qc rpkm) and BamFingerprint (--qc fpt)
  • various GNU utilities - ex: gzip, grep, mv, cp, rm, awk, sort, cut, uniq, etc. (this is not a complete list, but most users should not have a problem here)

lmod managed systems

When running on systems where packages are managed by a system such a lmod, several modules must be loaded prior to running. For the system perceval.rutgers.edu a the below module load command should be used:

module load java/1.8.0_121 samtools/0.1.19 intel/17.0.2 python/2.7.12 bedtools2/2.25.0 R-Project/3.3.3 bowtie2/2.2.9

Sample Manifest

The scripts takes as a required positional argument a sample manifest file in tab-separated format with the following column headers (case-sensitive):

Path	Basename	PE	Genome	Dest
/path/to/fastq	anti_H3K18Ac_K562_WCE_CAGATC_ALL	True	hg19	/path/to/bam/dest

Where:

Column Name Description
Path Directory where FASTQ files are located
Basename Basename of the sample, without read or lane information
PE Truthy (true/1) if sample is paired-end, Falsey (false/0) is sample is singe end reads
Genome Reference genome to use for sample
Dest Destination directory for pipeline output

Clone this wiki locally