rnaseqhs 0.3

Tool for analysis of RNA-seq data.

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.