miRNA-seq Tuxedo Modules
Modules available in the miRNA-seq Tuxedo 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:
TopHat
-
omics_pipe.modules.tophat.tophat(sample, tophat_flag)[source]
Runs TopHat to align .fastq files.
- input:
- .fastq file
- output:
- accepted_hits.bam
- citation:
- Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics doi:10.1093/bioinformatics/btp120
- link:
- http://tophat.cbcb.umd.edu/
- parameters from parameters file:
RAW_DATA_DIR:
REF_GENES:
TOPHAT_RESULTS:
BOWTIE_INDEX:
TOPHAT_VERSION:
TOPHAT_OPTIONS:
Cufflinks
-
omics_pipe.modules.cufflinks.cufflinks(sample, cufflinks_flag)[source]
Runs cufflinks to assemble .bam files from TopHat.
- input:
- accepted_hits.bam
- output:
- transcripts.gtf
- citation:
- Trapnell C, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology doi:10.1038/nbt.1621
- link:
- http://cufflinks.cbcb.umd.edu/
- parameters from parameters file:
TOPHAT_RESULTS:
CUFFLINKS_RESULTS:
REF_GENES:
GENOME:
CUFFLINKS_OPTIONS:
CUFFLINKS_VERSION:
Cuffmerge
-
omics_pipe.modules.cuffmerge.cuffmerge(step, cuffmerge_flag)[source]
Runs cuffmerge to merge .gtf files from Cufflinks.
- input:
- assembly_GTF_list.txt
- output:
- merged.gtf
- citation:
- Trapnell C, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology doi:10.1038/nbt.1621
- link:
- http://cufflinks.cbcb.umd.edu/
- parameters from parameters file:
CUFFMERGE_RESULTS:
REF_GENES:
GENOME:
CUFFMERGE_OPTIONS:
CUFFLINKS_VERSION:
Cuffmergetocompare
-
omics_pipe.modules.cuffmergetocompare.cuffmergetocompare(step, cuffmergetocompare_flag)[source]
Runs cuffcompare to annotate merged .gtf files from Cufflinks.
- input:
- assembly_GTF_list.txt
- output:
- merged.gtf
- citation:
- Trapnell C, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology doi:10.1038/nbt.1621
- link:
- http://cufflinks.cbcb.umd.edu/
- parameters from parameters file:
CUFFMERGE_RESULTS:
REF_GENES:
GENOME:
CUFFMERGETOCOMPARE_OPTIONS:
CUFFLINKS_VERSION:
Cuffdiff
-
omics_pipe.modules.cuffdiff.cuffdiff(step, cuffdiff_flag)[source]
Runs Cuffdiff to perform differential expression. Runs after Cufflinks. Part of Tuxedo Suite.
- input:
- .bam files
- output:
- differential expression results
- citation:
- Trapnell C, et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Nature Biotechnology doi:10.1038/nbt.1621
- link:
- http://cufflinks.cbcb.umd.edu/
- parameters from parameters file:
CUFFDIFF_RESULTS:
GENOME:
CUFFDIFF_OPTIONS:
CUFFMERGE_RESULTS:
CUFFDIFF_INPUT_LIST_COND1:
CUFFDIFF_INPUT_LIST_COND2:
CUFFLINKS_VERSION:
R Summary Report
-
omics_pipe.modules.RNAseq_report_tuxedo.RNAseq_report_tuxedo(sample, RNAseq_report_tuxedo_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: