rnaseqhs 0.3
Tool for analysis of RNA-seq data.
License: MIT
Keywords: rnaseq main

rnaseqhs
=========

overview
---------
rnaseqhs can do bioinformatics analysis for RNA_seq data and generate clean BAM/SAM result from HISAT2, GTF result from Stringtie and featureCounts result. 

rnaseqhs is available under the terms of the MIT license (see the file ``LICENSE``)

pre-requirements
-----------------
1. 'gzip','fastx_trimmer','fastqc','cutadapt','fastq_quality_filter','hisat2','stringtie','samtools (v1.3.1)','bedtools (v2.19.1)' in $PATH.
2.  hisat2 built genome index, transcriptome index, and gtf.

Installation
-------------
1. tar zxvf rnaseqhs-<version>.tar.gz
2. cd rnaseqhs-<version>
3. python setup.py install --user

Usage
------
1. use it as module in python console ::

    >>>import rnaseqhs

    >>>rnaseqhs.rnaseqhs.main(<Arguments>)

Arguments are ::
    >>>rnaseqhs.rnaseqhs.main(NDIR,OUTDIR,PHRED,QCCHECK,TRIM,LASTKEEP,RMADAPT, LADAPTER, RADAPTER
                ,OVERLAP,MINLEN,REMOVEN,NCUTOFF,FILTQ
                ,MINQ,PMINQ,QCSTAT,MAPPING,HISAT2INDEX,ORIENTATIONS
                ,RNASTRANDNESS,GTF,RAWCOVER,GENOMEBED,WINDOWSIZE])

2. use it as command line in bash ::

    <installed-path>/rnaseqhsb <options>

Options are ::
usage: rnaseqhs [-h] [-i INDIR] [-o OUTDIR] [-P PHRED] [-Q QCCHECK] [-T TRIM]
                [-l LASTKEEP] [-r RMADAPT] [-L LADAPTER] [-R RADAPTER]
                [-O OVERLAP] [-m MINLEN] [-N REMOVEN] [-c NCUTOFF] [-F FILTQ]
                [--minQ MINQ] [--pminQ PMINQ] [-q QCSTAT] [-M MAPPING]
                [--hisat2index HISAT2INDEX] [--orientations ORIENTATIONS]
                [--rnastrandness RNASTRANDNESS] [--gtf GTF]
                [--drawCover DRAWCOVER] [--genomebed GENOMEBED]
                [--windowsize WINDOWSIZE]

optional arguments:
  -h, --help            show this help message and exit
  -i INDIR, --indir INDIR
                        fastq files path
  -o OUTDIR, --outdir OUTDIR
                        output path
  -P PHRED, --phred PHRED
                        phred score used in platform [33]
  -Q QCCHECK, --qccheck QCCHECK
                        do quality check [true]
  -T TRIM, --trim TRIM  trim given fastq short reads as --lastkeep defined
  -l LASTKEEP, --lastkeep LASTKEEP
                        with "trim" option, last bases to keep
  -r RMADAPT, --rmadapt RMADAPT
                        remove adapter [true]
  -L LADAPTER, --ladapter LADAPTER
                        left adapter [AGATCGGAAGAGC]
  -R RADAPTER, --radapter RADAPTER
                        right adapter [AGATCGGAAGAGC]
  -O OVERLAP, --overlap OVERLAP
                        If the overlap between the read and adapter is shorter
                        than the overlap length, the read will NOT be
                        modified. [6]
  -m MINLEN, --minlen MINLEN
                        Discard trimmed reads that are shorter than "minlen"
                        [75]
  -N REMOVEN, --removeN REMOVEN
                        remove "N" bases [true]
  -c NCUTOFF, --Ncutoff NCUTOFF
                        with "removeN" option, N cutoff [0.1]
  -F FILTQ, --filtQ FILTQ
                        Filters sequences based on quality [true]
  --minQ MINQ           Minimum quality score to keep [20]
  --pminQ PMINQ         Minimum percent of bases [80]
  -q QCSTAT, --qcStat QCSTAT
                        generate QC statistic plot for seq
  -M MAPPING, --mapping MAPPING
                        read mapping [true]
  --hisat2index HISAT2INDEX
                        hisat2 index
  --orientations ORIENTATIONS
                        orientations
  --rnastrandness RNASTRANDNESS
                        rna strandness
  --gtf GTF             gtf file for annotation
  --drawCover DRAWCOVER
                        coverage of genome region [true]
  --genomebed GENOMEBED
                        coverage genome bed file
  --windowsize WINDOWSIZE
                        coverage window size [500000]

Links
-----

* `Project homepage <https://git-r3lab.uni.lu/zhi.zhang/rnaseqhs>`_
* `Github page <https://git-r3lab.uni.lu/zhi.zhang/rnaseqhs>`_
    written by Zhi Zhang.