miRNA-seq Count Based Modules
Modules available in the count-based miRNA-seq Pipeline.
CutAdapt
-
omics_pipe.modules.cutadapt_miRNA.cutadapt_miRNA(sample, cutadapt_miRNA_flag)[source]
Runs Cutadapt to trim adapters from reads.
- input:
- .fastq
- output:
- .fastq
- citation:
- Martin 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17: 10-12.
- link:
- https://code.google.com/p/cutadapt/
- parameters from parameters file:
- sample, RAW_DATA_DIR, ADAPTER, TRIMMED_DATA_PATH
Fastq Length Filter
-
omics_pipe.modules.fastq_length_filter_miRNA.fastq_length_filter_miRNA(sample, fastq_length_filter_miRNA_flag)[source]
Runs custom Python script to filter miRNA reads by length.
- input:
- .fastq
- output:
- .fastq
- parameters from parameter file:
- TRIMMED_DATA_PATH:
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:
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:
HTSEQ
-
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:
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:
DPS_VERSION:
PARAMS_FILE: