######## Title ########
Bioinformatics Scripts and Datasets


######## Requirement ########
* fastx_trimmer version 0.0.14
* SailfishBeta version 0.10.0 CentOS5
* ensembl76 reference dataset
* HISAT2 version 2.0.4
* samtools version 0.1.19
* hg38 index of HISAT2
* samtools version 1.3
* bedtools version v2.25.0
* RSeQC version 2.6.4
* WiggleTools
* wigToBigWig
* ngsplot
* csfq2fq.pl
* bowtie2 version 2-2.3.5.1
* BEDOPS v2.4.39
* liftOver and "hg19ToHg38.over.chain"
* juicer ("https://github.com/aidenlab/juicer")


######## Usage ########
Usage : Please see following script list.
Some parts need to be edited by yourself.


######## Script List ########
* 01_RNA.sh : Process of RNA-seq analysis.
* 02_fraction.sh : Process of chromatin compaction analysis.
* 03_nucleosome.sh : Process of nucleosome occupancy analysis.
* 04_polymerase.sh : Process of profile of RNA-polymerase II binding level analysis.
* 05_HIC.sh : Process of HIC analysis.


######## Item List ########
The items dorectory contains several files to execute commands of those script.
* hg38_rmsk.bed : Bed format datas of repetitive sequence of hg38.
* hg38_GENCODE_v23.bed : Bed format datas of hg38 genome annotation.
* read_dist.cln.tsv : integrated data of HepG2_F?_rd.txt
* read_dist_cln.R : R script of hierarchical clustering of the compotition rate of fractions.
* hg38.chrom.sizes : List of chromosome sizes of hg38.
* config_all.txt : Configuration file (all genes) of ngs.plot.r for fractional proportion analysis.
* config_high.txt : Configuration file (high transcription levels) of ngs.plot.r for fractional proportion analysis.
* config_mid.txt : Configuration file (mid transcription levels) of ngs.plot.r for fractional proportion analysis.
* config_low.txt : Configuration file (low transcription levels) of ngs.plot.r for fractional proportion analysis.
* config_all_nuc.txt : Configuration file (all genes) of ngs.plot.r for nucleosome occupancy analysis.
* config_high_nuc.txt : Configuration file (high transcription levels) of ngs.plot.r for nucleosome occupancy analysis.
* config_mid_nuc.txt : Configuration file (mid transcription levels) of ngs.plot.r for nucleosome occupancy analysis.
* config_low_nuc.txt : Configuration file (low transcription levels) of ngs.plot.r for nucleosome occupancy analysis.
* config_all_pol.txt : Configuration file (all genes) of ngs.plot.r for RNA-polymerase II binding level analysis.
* config_high_pol.txt : Configuration file (high transcription levels) of ngs.plot.r for RNA-polymerase II binding level analysis.
* config_mid_pol.txt : Configuration file (mid transcription levels) of ngs.plot.r for RNA-polymerase II binding level analysis.
* config_low_pol.txt : Configuration file (low transcription levels) of ngs.plot.r for RNA-polymerase II binding level analysis.
* sizes.genome : List of chromosome sizes of hg38 (used in "05_HIC.sh")
* hg38_HindIII.txt : Restriction site file of HIC analysis.


######## Author ########
Takeru Kameda and Itoshi Nikaido
Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research (https://bit.riken.jp)


######## License ########
Copyright 2020 Takeru Kameda and Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.