RNA-seq Count Based Modules

Modules available in the count-based RNA-seq Pipeline.

FASTQC

omics_pipe.modules.fastqc.fastqc(sample, fastqc_flag)[source]

QC check of raw .fastq files using FASTQC.

input:
.fastq file
output:
folder and zipped folder containing html, txt and image files
citation:
Babraham Bioinformatics
link:
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
parameters from parameters file:

RAW_DATA_DIR:

QC_PATH:

FASTQC_VERSION:

COMPRESSION:

STAR Aligner

omics_pipe.modules.star.star(sample, star_flag)[source]

Runs STAR to align .fastq files.

input:
.fastq file
output:
Aligned.out.bam
citation:
  1. Dobin et al, Bioinformatics 2012; doi: 10.1093/bioinformatics/bts635 “STAR: ultrafast universal RNA-seq aligner”
link:
https://code.google.com/p/rna-star/
parameters from parameters file:

ENDS:

RAW_DATA_DIR:

STAR_INDEX:

STAR_OPTIONS:

STAR_RESULTS:

SAMTOOLS_VERSION:

STAR_VERSION:

COMPRESSION:

REF_GENES:

HTSEQ-count

omics_pipe.modules.htseq.htseq(sample, htseq_flag)[source]

Runs htseq-count to get raw count data from alignments.

input:
Aligned.out.sort.bam
output:
counts.txt
citation:
Simon Anders, EMBL
link:
http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html
parameters from parameters file:

STAR_RESULTS:

HTSEQ_OPTIONS:

REF_GENES:

HTSEQ_RESULTS:

TEMP_DIR:

SAMTOOLS_VERSION:

BAM_FILE_NAME:

PYTHON_VERSION:

R Summary Report - DESEQ2

omics_pipe.modules.RNAseq_report_counts.RNAseq_report_counts(sample, RNAseq_report_counts_flag)[source]

Runs R script with knitr to produce report from RNAseq pipeline.

input:
results from other steps in RNAseq pipelines
output:
html report
citation:
  1. Meissner
parameters from parameter file:

WORKING_DIR:

R_VERSION:

REPORT_RESULTS:

PARAMS_FILE: