RNA-seq Count Based Modules- TCGA¶
Modules available in the TCGA count-based RNA-seq Pipeline.
TCGA Download¶
- omics_pipe.modules.TCGA_download.TCGA_download(sample, TCGA_download_flag)[source]¶
Downloads and unzips TCGA data from Manifest.xml downloaded from CGHub. input:
TGCA XML file- output:
- downloaded files from TCGA
- citation:
- The Cancer Genome Atlas
- link:
- https://cghub.ucsc.edu/software/downloads.html
- parameters from parameters file:
TCGA_XML_FILE:
TCGA_KEY:
TCGA_OUTPUT_PATH:
CGATOOLS_VERSION:
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:
- 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:
- Meissner
- parameters from parameter file:
WORKING_DIR:
R_VERSION:
REPORT_RESULTS:
PARAMS_FILE: