rnalysis.fastq

Description

The fastq module provides a unified programmatic interface to external tools that process FASTQ files. Those currently include the CutAdapt adapter-trimming tool, the kallisto RNA-sequencing quantification tool, the bowtie2 alignment tool, and the featureCounts feature counting tool.

Classes

PairedEndPipeline()
SingleEndPipeline()

Functions

bowtie2_align_paired_end(r1_files, r2_files, ...)	Align paired-end reads from FASTQ files to a reference sequence using the bowtie2 aligner.
bowtie2_align_single_end(fastq_folder, ...)	Align single-end reads from FASTQ files to a reference sequence using the bowtie2 aligner.
bowtie2_create_index(genome_fastas, ...[, ...])	builds a bowtie index from FASTA formatted files of target sequences (genome).
convert_sam_format(input_folder, output_folder)	Convert SAM files to BAM files or vice versa using Picard SamFormatConverter.
create_bam_index(input_folder, output_folder)
fastq_to_sam_paired(r1_files, r2_files, ...)	Convert SAM/BAM files to FASTQ files using Picard SamToFastq.
fastq_to_sam_single(input_folder, output_folder)	Convert SAM/BAM files to FASTQ files using Picard SamToFastq.
featurecounts_paired_end(input_folder, ...)	Assign mapped paired-end sequencing reads to specified genomic features using RSubread featureCounts.
featurecounts_single_end(input_folder, ...)	Assign mapped single-end sequencing reads to specified genomic features using RSubread featureCounts.
find_duplicates(input_folder, output_folder)	Find duplicate reads in SAM/BAM files using Picard MarkDuplicates.
kallisto_create_index(transcriptome_fasta[, ...])	builds a kallisto index from a FASTA formatted file of target sequences (transcriptome).
kallisto_quantify_paired_end(r1_files, ...)	Quantify transcript abundance in paired-end mRNA sequencing data using kallisto.
kallisto_quantify_single_end(fastq_folder, ...)	Quantify transcript abundance in single-end mRNA sequencing data using kallisto.
sam_to_fastq_paired(input_folder, output_folder)	Convert SAM/BAM files to FASTQ files using Picard SamToFastq.
sam_to_fastq_single(input_folder, output_folder)	Convert SAM/BAM files to FASTQ files using Picard SamToFastq.
shortstack_align_smallrna(fastq_folder, ...)	Align small RNA single-end reads from FASTQ files to a reference sequence using the ShortStack aligner (version 4).
sort_sam(input_folder, output_folder[, ...])	Sort SAM/BAM files using Picard SortSam.
trim_adapters_paired_end(r1_files, r2_files, ...)	Trim adapters from paired-end reads using CutAdapt.
trim_adapters_single_end(fastq_folder, ...)	Trim adapters from single-end reads using CutAdapt.
validate_sam(input_folder, output_folder[, ...])	Validate SAM/BAM files using Picard ValidateSamFile.