rnalysis.fastq
==============

.. rubric:: Description

.. automodule:: rnalysis.fastq

.. currentmodule:: rnalysis.fastq


.. rubric:: Classes

.. autosummary::
    :toctree: .
    
    PairedEndPipeline
    SingleEndPipeline




.. rubric:: Functions

.. autosummary::
    :toctree: .
    
    bowtie2_align_paired_end
    
    bowtie2_align_single_end
    
    bowtie2_create_index
    
    convert_sam_format
    
    create_bam_index
    
    fastq_to_sam_paired
    
    fastq_to_sam_single
    
    featurecounts_paired_end
    
    featurecounts_single_end
    
    find_duplicates
    
    kallisto_create_index
    
    kallisto_quantify_paired_end
    
    kallisto_quantify_single_end
    
    sam_to_fastq_paired
    
    sam_to_fastq_single
    
    shortstack_align_smallrna
    
    sort_sam
    
    trim_adapters_paired_end
    
    trim_adapters_single_end
    
    validate_sam