User guide

Welcome to phasihunter 😉

A multithreaded program for mining phasiRNA regulation pathways based on multiple reference sequences.

PhasiHunter workflow

Dependencies

phasihunter is a CLI program runing on linux platform. The correction runing of phasihunter depends on some existing softwares.

Bowtie (Langmead, et al., 2009. Genome Biol)
Bedtools (Quinlan and Hall, 2010. Bioinformatics)
Dnapi (Tsuji and Weng, 2016. PloS One)
Trim_galore (https://github.com/FelixKrueger/TrimGalore)
Seqkit (Shen, et al., 2016. PloS One)
Perl5 (https://www.perl.org)
Fasta36 (Pearson and Lipman, 1988. Proc Natl Acad Sci U S A)
TarHunter (Ma, et al., 2018. Bioinformatics)

Python packages also required:

Biopython (Cock, et al., 2009. Bioinformatics)
pyyaml
matplotlib
sympy

Installation

Manual Installation

Clone phasihunter repository

Using git:

git clone https://github.com/HuangLab-CBI/PhasiHunter.git

Install all dependencies

You can manually install each dependency listed above, or alternatively a conda environment file is provided in this repositoty (environment.yml), and can be used to install the dependencies with the following command:

conda env create  --file environment.yml

(If you have mamba installed you can replace conda in the above command with mamba.)

Access the dependencies using:

conda activate phasiHunter

Adding the executable to your $PATH

If you are using conda you can simply symlink the phasiHunter executable to the conda environment bin. In the activated conda environemnt, run:

ln -s <full path to phasiHunter directory>/phasiHunter $CONDA_PREFIX/bin/phasiHunter

Otherwise you can add phasiHunter to your PATH by setting the enviroment variable in ~/.bashrc

echo "export PATH=$PATH:<phasihunter PATH> >> ~/.bashrc"

example:

echo "export PATH=$PATH:/home/user/volumes/PhasiHunter >> ~/.bashrc"

type phasiHunter -h to check whether the installation was correct. If phasiHunter is installed correctly you will see the following content.

Docker image

For convenience, we also provide a Docker image at https://hub.docker.com/repository/docker/zacksfeng/phasihunter

The Docker image has been configured with all the dependencies required for running phasiHunter.

Demo data

Download link

https://cbi.njau.edu.cn/PhasiHunter_demo_data/test_osa.tar.gz

Executing PhasiHunter with step-by-step submodules.

Parameter in < > means necessary; parameter in [ ] means optional

Data pre-process

phasiHunter preprocess -m r -i /home/user/test_osa/SRR5049781.fastq.gz -mi 19 -ma 25 -e 1 -n 1000000 -o /home/user/test_osa/SRR5049781_processed_cdna.map -in /home/user/test_osa/index/oryza_sativa_cdna_index

phasiHunter preprocess -m m -i /home/user/test_osa/SRR5049781_trimmed_format_filter.fa -mi 19 -ma 25 -e 1 -n 1000000 -o /home/user/test_osa/SRR5049781_processed_gdna.map -in /home/user/test_osa/index/oryza_sativa_gdna_index

preprocess module usage

Help messeage:
  options: 
    # necessary options:
    -m:  string --  mode: r | c | m;
                    raw(mode): trim adaptor --> normalization --> length and abundance filter --> mapping
                    clean(mode): normalization --> length and abundance filter --> mapping
                    mapping(mode): mapping
    -i:  file   --  for r mode: fastq file or fastq.gz file
                    for c mode: fasta file or fasta.gz file
                    for m mode: length and abundance filter fasta file
    -r:  file   --  reference sequence fasta file
    -in: string --  index prefix, -r option will be ignored when -in enable
    -o:  outfile --  outfile name

    # options with default value
    -j:  int    --  adaptor trim parallel cores; <8 is recommend, only need in r mode, default=1
    -bj: int    --  bowtie parallel cores; defalut=1
    -mh: int    --  max hits when mapping to ref sequence, default=10
    -mi: int    --  minimal sRNA reads length cutoff, default=19
    -ma: int    --  maxmial sRNA reads length cutoff, default=25
    -e:  float  --  sRNA reads cpm cutoff, default=1 
    -n:  int    --  normalization base, default=1000000


    # other
    -v:         --  print version information
    -h:         --  print help information

PhasiRNA and PHAS loci prediction

phasiHunter phase -cm /home/user/test_osa/SRR5049781_processed_cdna.map -c /home/user/test_osa/oryza_sativa_cdna.fa -gm /home/user/test_osa/SRR5049781_processed_gdna.map -g /home/user/test_osa/oryza_sativa_gdna.fa -fm None -f None -fa /home/user/test_osa/SRR5049781_trimmed_format_filter.fa -a /home/user/test_osa/phase_a.txt -o /home/user/test_osa/phase_o.txt -me b -il 5 -pl 21 -pn 4 -mh 10 -j 20 -pv 0.001 -ps 15 -pr 0.4 -cl y

phase module usage

phase usage:
  option:
    -cm: file  --  map file based on reference transcriptome sequence
    -c:  file  --  reference transcritome sequence, fasta file
    -gm: file  --  map file based on reference genome sequence
    -g:  file  --  reference genome sequence, fasta file
    -fm: file  --  map file based on full length transcriptome sequence
    -f:  file  --  full length transcriptome sequence, fasta file
    -fa: file  --  sRNA file
    -a:  out   --  allsiRNA cluster output file, default name is phase_a.txt
    -o:  out   --  phasiRNA cluster output file, default name is phase_o.txt
    -me: str   --  phasiRNA prediction method, h(hypergeometric test) | p(phase score) | b (both), default=b
    -il: int   --  phasiRNA cluster island, default=5
    -pl: int   --  phase length, 21 | 24, default=21
    -pn: int   --  phase number, default=4
    -mh: int   --  max hits when mapping to ref sequence, default=10
    -j:  int   --  parallel number, default=1
    -pv: float --  pvalue cutoff, default=0.001, only function with h/b method applied
    -ps: float --  phase score cutoff, default=15, only function with p/b method applied
    -pr: float --  phase ratio cutoff, default=0.4, only function with p/b method applied
    -cl: str   --  delete .phasiHuter_bowtieIndex, y|n, default=y
    -v:        --  print version information
    -h:        --  print help information

PhasiRNA and PHAS loci result integration

phasiHunter integration -io /home/user/test_osa/phase_o.txt -ia /home/user/test_osa/phase_a.txt -an /home/user/test_osa/oryza_sativa_gdna.gff3 -g y -o /home/user/test_osa/integration_o.txt -a /home/user/test_osa/integration_a.txt -s /home/user/test_osa/integration_s.txt -po /home/user/test_osa/integration_p.txt -j 1 -pn 4 -pl 21 -pv 0.001 -il 5

integration module usage

integration usage:
  option:
    # necessary options:
    -io: file  --  phase module -o output file
    -ia: file  --  phase module -a output file
    -an: file  --  reference genome gff3 file
    -g:  str   --  y | n, whether exist gdna based PHAS Loci

    # options with default value
    -o:  out  --  integration phasiRNA cluster, default name is integration_o.txt
    -a:  out  --  integration all siRNA cluster, default name is integration_a.txt
    -s:  out  --  integration summary, default name is integration_s.txt
    -po: out  --  PHAS Loci information, default name is integration_p.txt
    -j:  int   --  parallel number, default=1
    -pn: int   --  phase number, default=4
    -pl: int   --  phase length, 21 | 24, default=21
    -pv: float --  pvalue cutoff, default=0.001
    -il: int   --  phasiRNA cluster island, default=5
    -dp: str   -- y | n, discard only P method result, default=y

    # optional options
    -fn: file  --  full length transcript annotation file

    # other
    -v:       --  print version information
    -h:       --  print help information

Print phasiRNA_cluster plot, phasiRNA.fa, PHAS.fa

phasiHunter visulization -io /home/user/test_osa/integration_o.txt -ia /home/user/test_osa/integration_a.txt -ip /home/user/test_osa/integration_p.txt -a /home/user/test_osa/alignment.txt -o /home/user/test_osa/phasiRNA.fa -p /home/user/test_osa/PHAS.fa -pl 21 -m 10 -c /home/user/test_osa/oryza_sativa_cdna.fa -g /home/user/test_osa/oryza_sativa_gdna.fa -f None -pc y -pg y -pf n

visulization module usage

visulization usage:
  option:
    # necessary options:
    -io: file  --  integration -io outputfile
    -ia: file  --  integration -ia outputfile
    -ip: file  --  integration -po outputfile
    -a:  out   --  alignment file, default name is alignment.txt
    -o:  out   --  phasiRNA fasta file, default name is phasiRNA.fa
    -p:  out   --  PHAS Gene fasta file; Format: >geneid/chr\tphasiRNA_cluster_region(start end)\tseq_region(start end), default name is PHAS.fa

    # options with default value
    -pl: int   --  phase length, 21 | 24, default=21
    -m:  float  --  the number for reducing the size of Y-axis. default=10

    # optional options
    -c:  file  --  reference transcritome sequence, fasta file, enable cdna based phasiRNA.fa, PHAS.fa, Alignmen, Plot output
    -g:  file  --  reference genome sequence, fasta file, enable gdna based phasiRNA.fa, PHAS.fa, Alignmen, Plot output
    -f:  file  --  full length transcriptome sequence, fasta file, enable flnc based phasiRNA.fa, PHAS.fa, Alignmen, Plot output
    -pc: str  --  plot cdna based phasiRNA cluster, y | n, defaut=y
    -pg: str  --  plot gdna based phasiRNA cluster, y | n, defaut=y
    -pf: str  --  plot flnc based phasiRNA cluster, y | n, defaut=y

    # other
    -v:        --  print version information
    -h:        --  print help information

Initiator prediction and verification

phasiHunter target -q /home/user/test_osa/osa.miRbase.fa -b /home/user/test_osa/PHAS.fa -o /home/user/test_osa/miR_target.txt -T 10

phasiHunter initiator -i /home/user/test_osa/integration_o.txt -j /home/user/test_osa/miR_target.txt -ip /home/user/test_osa/integration_p.txt -pd 5 -pl 21 -ps 1 -o /home/user/test_osa/initiator.txt

phasiHunter deg -i /home/user/test_osa/deg/GSM1040649_format_filter.map -q /home/user/test_osa/osa.miRbase.fa -j /home/user/test_osa/initiator.txt -t /home/user/test_osa/oryza_sativa_cdna.fa -o GSM1040649_MTI_deg.txt -s 1 -m 0 -p y -in y -pl 1 -pf MTI_deg --lib GSM1040649 -less

target module usage

Usage:
    perl /home/user/volumes/PhasiHunter/bin/TarHunterL_Modified.pl -q <mir_file> -b <targ_file> -o <out_file> [Options]

Required arguments:
    -q (--qmir):         query miRNA file
    -b (--targ):         target file
    -o (--output):       output file

Options:

    -M (--total_misp):   max. total mispairs               [Default: off]
    -m (--seed_misp):    max. seed mispairs                [Default: off]
    -f (--score):        score cutoff                      [Default:  4 ]

    -I (--mimics):       eTM search                        [Default: off]
    -i (--mimics_str):   eTM stringency
                        (0: strict, 1: relaxed)           [Default:  0 ]

    -T (--threads):      FASTA threads                     [Default:  1 ]
    -t (--tab):          tabular format output             [Default: off]
    -h (--help):         help information

Dependencies:
    fasta36

initiator module usage

initiator option:
  -i  [str]integration -o output
  -j  [str]the target predicted by psRNAtarget server or target module
  -ip [str]integration -po output
  -pd [int]the microRNA distance away to phase border, default=105(21) or 120 (24), optional
  -pl [int]21 or 24, the phase length of 21 or 24, default=21
  -ps [int]0 or 1, the position of cleavage at 10(0) or 9-11 (1), default=1
  -o  [str]outputfilename.
  -h  print the version and details of the usage

deg module usage

// function: vertified the sRNA - Target interaction with degradome data

  options:
  -i: <inputfilename>     --    mapping file for degradome data mapping transcripts, by bowtie
  -q: <sRNA fasta>        --    small RNA sequences used for target prediction, fasta
  -j: <inputfilename>     --    from psRNATarget batch download file or initiator output
  -t: <inputfilename>     --    transcripts file, fasta
  -o: <outputfilename>    --    matched map file with only matched records
  -s: <shift_number>      --    if shifts=0 then cleaved exactly at pos.10, default=1
  -m: <minum deg_num>     --    minum number of degradome reads, int, default=0
  -p: <T-plot function>   --    enable the plot function, y | n, default='n' 
  -in: <bool>             --    y | n, use initiator output information
  -pl [int]               --    1,plot only category 1; 2, plot categories 1 and 2, default=1
  -pf [str]               --    output folder name, for exporting t-plot images and outputfile
  --lib [str]             --    library name
  -less                   --    only output cat_1 and cat_2 information

  ***********************
  //About the categories:
  Cat #1, degradome read at the cleavage site is most abundant.
  Cat #2, the read is less than the most abudant one, but higher than the median.
  Cat #3, the read is less than the median, but high than 1
  Cat #4, the read is identical or less than 1 (if degradome data is normalized)

PhasiRNA target prediction and verification

phasiHunter target -q /home/user/test_osa/phasiRNA.fa -b /home/user/test_osa/oryza_sativa_cdna.fa -o /home/user/test_osa/phasiRNA_target.txt -T 10

phasiHunter deg -i /home/user/test_osa/deg/GSM1040649_format_filter.map -q /home/user/test_osa/phasiRNA.fa -j /home/user/test_osa/phasiRNA_target.txt -t /home/user/test_osa/oryza_sativa_cdna.fa -o GSM1040649_PTI_deg.txt -s 1 -m 0 -p y -in n -pl 1 -pf PTI_deg --lib GSM1040649 -less

Executing PhasiHunter with one-command module

One-command module usage

One command executing mode

Usage: 
    phasiHunter run [-i] [config file]
    phasiHunter run -d

option:
    -i: yaml format config file
    -d: using the default config, defalut config file is /foo/PhasiHunter/bin/config.yaml
    -h: print help information

WARNIG: make sure choose the correct config file before run this command

Default config.yaml file

Some INPUT and OUTPUT still need modified when using.

# Please provide the full path to the input file

# Configure the modules that need to be run
# y means enable, n means disable
Runing_module:
  preprocess: y
  phase: y
  integration: y
  visulization: y
  initiator_prediction_and_verification:
    target: y
    initiator: y
    deg: y
  phasiRNA_target_prediction_and_verification:
    phasiRNA_target: y
    phasiRNA_deg: y

# Configure the preprocess module
preprocess:
  # raw(mode): trim adaptor --> normalization --> length and abundance filter --> mapping
  # clean(mode): normalization --> length and abundance filter --> mapping
  # mapping(mode): mapping
  mode: r # [r | c | m]

  # for r mode: fastq file or fastq.gz file
  # for c mode: fasta file or fasta.gz file
  # for m mode: length and abundance filter fasta file
  # ** INPUT ** 
  inputfile: /home/user/test_osa/SRR5049781.fastq.gz

  # reference sequence fasta file
  # ** INPUT ** 
  reference_fasta: # disable when index parameter enable, multiple sequence can provided here
    # - /home/user/test_osa/oryza_sativa_cdna.fa
    # - /home/user/test_osa/oryza_sativa_gdna.fa

  # index prefix, reference_fasta option will be ignored when index enable, multiple index can provided here
  # ** INPUT ** 
  index:
    - /home/user/test_osa/index/oryza_sativa_cdna_index
    - /home/user/test_osa/index/oryza_sativa_gdna_index

  # outfile name, relative path is work for outputfile, but absolute path is still recommended. The number must be the same as the number of reference_fasta or indexs
  # ** OUTPUT ** 
  outfile_name: 
    - /home/user/test_osa/SRR5049781_processed_cdna.map
    - /home/user/test_osa/SRR5049781_processed_gdna.map

  # adaptor trim parallel cores; <8 is recommend, only need in r mode
  trim_adaptor_cores: 1

  # bowtie parallel cores
  bowtie_mapping_cores: 1

  # max hits when mapping to ref sequence
  bowtie_max_hits_cutoff: 10

  # minimal sRNA reads length cutof
  minimal_sRNA_length_cutoff: 19

  # maxmial sRNA reads length cutoff
  maxmial_sRNA_length_cutoff: 25

  # sRNA reads cpm cutoff
  sRNA_expression_cutoff: 1

  # normalization base
  library_normalization_base: 1000000


# Configure the phase module
# predicting with only one reference sequence or multiple reference sequences
phase:
  # map file based on reference transcriptome sequence
  # ** INPUT ** 
  mapped_cdna_file: /home/user/test_osa/SRR5049781_processed_cdna.map

  # map file based on reference genome sequence
  # ** INPUT ** 
  mapped_gdna_file: /home/user/test_osa/SRR5049781_processed_gdna.map
  
  # map file based on full length transcriptome sequence
  # ** INPUT ** 
  mapped_flnc_file:

  # reference transcritome sequence, fasta file
  # ** INPUT ** 
  cdna_fasta: /home/user/test_osa/oryza_sativa_cdna.fa

  # reference genome sequence, fasta file
  # ** INPUT ** 
  gdna_fasta: /home/user/test_osa/oryza_sativa_gdna.fa
  
  # full length transcriptome sequence, fasta file
  # ** INPUT ** 
  flnc_fasta:

  # sRNA file
  # ** INPUT ** 
  sRNA_fa: /home/user/test_osa/SRR5049781_trimmed_format_filter.fa
  
  # allsiRNA cluster output
  # ** OUTPUT ** 
  allsiRNA_cluster_output: /home/user/test_osa/phase_a.txt
  
  # phasiRNA cluster output file
  # ** OUTPUT ** 
  phasiRNA_cluster_output: /home/user/test_osa/phase_o.txt
  
  # phasiRNA prediction method, h(hypergeometric test) | p(phase score) | b (both)
  phasiRNA_prediction_method: b

  # phasiRNA cluster island
  phasiRNA_cluster_island: 5

  # phase length
  phase_length: 21
  
  # phase number
  phase_number_cutoff: 4

  # max hits when mapping to ref sequence
  bowtie_max_hits_cutoff: 10

  # parallel number
  parallel_cores: 20

  # pvalue cutoff, only function with h/b method applied
  pvalue_cutoff: 0.001

  # phase score cutoff, only function with p/b method applied
  phase_score_cutoff: 15

  # phase ratio cutoff, only function with p/b method applied
  phase_ratio_cutoff: 0.4

  # delete .phasiHuter_bowtieIndex, y|n
  delete_index: y


# Configure the integration module
integration:
  # phase module phasiRNA_cluster_output
  # ** INPUT ** 
  o_inputfile: /home/user/test_osa/phase_o.txt

  # phase module allsiRNA_cluster_output
  # ** INPUT ** 
  a_inputfile: /home/user/test_osa/phase_a.txt

  # reference genome gff3 file
  # ** INPUT ** 
  gff3: /home/user/test_osa/oryza_sativa_gdna.gff3

  # y | n, whether exist gdna based PHAS Loci
  gdna_based_PHAS_Loci: y

  # integration phasiRNA cluster
  # ** OUTPUT ** 
  integration_phasiRNA_cluster: /home/user/test_osa/integration_o.txt

  # integration all siRNA cluste
  # ** OUTPUT ** 
  integration_allsiRNA_cluster: /home/user/test_osa/integration_a.txt

  # integration summary
  # ** OUTPUT ** 
  integration_summary: /home/user/test_osa/integration_s.txt

  # PHAS Loci information
  # ** OUTPUT ** 
  integration_PHAS_Loci_info: /home/user/test_osa/integration_p.txt

  # parallel number
  parallel_cores: 1

  # phase number
  phase_number_cutoff: 4

  # phase length
  phase_length: 21

  # pvalue cutoff
  pvalue_cutoff: 0.001

  # phasiRNA cluster island
  phasiRNA_cluster_island: 5

  # y | n, discard only P method result
  discard_only_P_method_result: y

  # full length transcript annotation file
  flnc_annotation_file:


# Configure the visulization module
visulization:
  # integration module integration_phasiRNA_cluster
  # ** INPUT ** 
  o_inputfile: /home/user/test_osa/integration_o.txt

  # integration module integration_allsiRNA_cluster
  # ** INPUT ** 
  a_inputfile: /home/user/test_osa/integration_a.txt

  # integration integration_PHAS_Loci_info
  # ** INPUT ** 
  p_inputfile: /home/user/test_osa/integration_p.txt

  # alignment file
  # ** OUTPUT ** 
  output_alignment_file: /home/user/test_osa/alignment.txt

  # phasiRNA fasta file
  # ** OUTPUT ** 
  output_phasiRNA_fa: /home/user/test_osa/phasiRNA.fa

  # PHAS Gene fasta file, Format: >geneid/chr\tphasiRNA_cluster_region(start end)\tseq_region(start end)
  # ** OUTPUT ** 
  output_PHAS_fa: /home/user/test_osa/PHAS.fa

  # phase length
  phase_length: 21

  # the number for reducing the size of Y-axis
  Y_axis: 10

  # reference transcritome sequence, fasta file, enable cdna based phasiRNA.fa, PHAS.fa, Alignmen, Plot output
  # ** INPUT ** 
  cdna_fasta: /home/user/test_osa/oryza_sativa_cdna.fa

  # reference genome sequence, fasta file, enable gdna based phasiRNA.fa, PHAS.fa, Alignmen, Plot output
  # ** INPUT ** 
  gdna_fasta: /home/user/test_osa/oryza_sativa_gdna.fa

  # full length transcriptome sequence, fasta file, enable flnc based phasiRNA.fa, PHAS.fa, Alignmen, Plot output
  # ** INPUT ** 
  flnc_fasta:

  # plot cdna based phasiRNA cluster, y | n
  plot_cdna_based_phasiRNA_cluster: y 

  # plot gdna based phasiRNA cluster, y | n
  plot_gdna_based_phasiRNA_cluster: y

  # plot flnc based phasiRNA cluster, y | n
  plot_flnc_based_phasiRNA_cluster: n


# Configure the target module
target:
  # query miRNA file, fasta format
  # ** INPUT ** 
  query_fa: /home/user/test_osa/osa.miRbase.fa

  # PHAS.fa/transcript.fa, fasta file
  # ** INPUT ** 
  subject_fa: /home/user/test_osa/PHAS.fa

  # output file
  # ** OUTPUT ** 
  output: /home/user/test_osa/miR_target.txt

  # max. total mispairs
  total_misp: off

  # max. seed mispairs
  seed_misp: off

  # score cutoff
  score: 4

  # eTM search 
  mimics: off

  # eTM stringency, (0: strict, 1: relaxed)
  mimics_str: 0

  # fasta36 threads
  threads: 10


# Configure the initiator module
initiator:
  # integration module integration_phasiRNA_cluster
  # ** INPUT ** 
  i_input_file: /home/user/test_osa/integration_o.txt

  # the target predicted by psRNAtarget server or target module
  # ** INPUT ** 
  j_input_file: /home/user/test_osa/miR_target.txt

  # integration module integration_PHAS_Loci_info
  # ** INPUT ** 
  p_input_file: /home/user/test_osa/integration_p.txt

  # the microRNA distance away to phase border, default=105(21) or 120 (24)
  sRNA_distance: 5

  # 21 or 24, the phase length of 21 or 24,
  phase_length: 21

  # 0 or 1, the position of cleavage at 10(0) or 9-11 (1)
  cleavage_shift: 1

  # outputfilename
  # ** OUTPUT ** 
  outputfile: /home/user/test_osa/initiator.txt


# Configure the deg module
deg:
  # mapping file for degradome data mapping transcripts, by bowtie
  # ** INPUT ** 
  inputfile: 
    - /home/user/test_osa/deg/GSM1040649_format_filter.map
    - /home/user/test_osa/deg/GSM1040650_format_filter.map
  
  # miRNA sequences used for target prediction, fasta
  # ** INPUT ** 
  query_fa: /home/user/test_osa/osa.miRbase.fa

  # initiator module outputfile
  # ** INPUT ** 
  STI_result: /home/user/test_osa/initiator.txt

  # transcripts file, fasta
  # ** INPUT ** 
  transcript_fa: /home/user/test_osa/oryza_sativa_cdna.fa

  # matched map file with only matched records
  # filename only, do not input directory
  # ** OUTPUT ** 
  output: 
    - GSM1040649_MTI_deg.txt
    - GSM1040650_MTI_deg.txt
  
  # if shifts=0 then cleaved exactly at pos.10
  shift: 1

  # minum number of degradome reads, int
  minum_deg_abun: 0

  # enable the plot function, y | n
  T_plot: y

  # y | n, use initiator output information
  initiator: y

  # 1,plot only category 1; 2, plot categories 1 and 2
  plot_categories: 1

  # output folder name, for exporting t-plot images and outputfile
  plot_folder: MTI_deg

  # library name
  library:
    - GSM1040649
    - GSM1040650
  
  # only output cat_1 and cat_2 information
  less: y


# Configure the phasiRNA_target module
phasiRNA_target:
  # query phasiRNA file, fasta format
  # ** INPUT ** 
  query_fa: /home/user/test_osa/phasiRNA.fa

  # target file, fasta file
  # ** INPUT ** 
  subject_fa: /home/user/test_osa/oryza_sativa_cdna.fa

  # output file
  # ** OUTPUT ** 
  output: /home/user/test_osa/phasiRNA_target.txt

  # max. total mispairs
  total_misp: off

  # max. seed mispairs
  seed_misp: off

  # score cutoff
  score: 4

  # eTM search 
  mimics: off

  # eTM stringency, (0: strict, 1: relaxed)
  mimics_str: 0

  # fasta36 threads
  threads: 10


# Configure the phasiRNA_deg module
phasiRNA_deg:
  # mapping file for degradome data mapping transcripts, by bowtie
  # ** INPUT ** 
  inputfile: 
    - /home/user/test_osa/deg/GSM1040649_format_filter.map
    - /home/user/test_osa/deg/GSM1040650_format_filter.map

  # phasiRNA sequences used for target prediction, fasta
  # ** INPUT ** 
  query_fa: /home/user/test_osa/phasiRNA.fa

  # psRNATarget/target outputfile
  # ** INPUT ** 
  STI_result: /home/user/test_osa/phasiRNA_target.txt

  # transcripts file, fasta
  # ** INPUT ** 
  transcript_fa: /home/user/test_osa/oryza_sativa_cdna.fa

  # matched map file with only matched records
  # filename only, do not input directory
  # ** OUTPUT ** 
  output: 
    - GSM1040649_PTI_deg.txt
    - GSM1040650_PTI_deg.txt
  
  # if shifts=0 then cleaved exactly at pos.10
  shift: 1

  # minum number of degradome reads, int
  minum_deg_abun: 0

  # enable the plot function, y | n
  T_plot: y

  # y | n, use initiator output information, for phasiRNA_deg, it must be n
  initiator: n

  # 1,plot only category 1; 2, plot categories 1 and 2
  plot_categories: 1

  # output folder name, for exporting t-plot images and outputfile
  plot_folder: PTI_deg

  # library name
  library:
    - GSM1040649
    - GSM1040650

  # only output cat_1 and cat_2 information
  less: y

The main output file

preprocess module
- preprocessed fasta file
- alignment file generated by bowtie
phase module
- redundant allsiRNA cluster output
  - table header: gene, strand, sRNA_position, sRNA_abundance, sRNA_record, sRNA_sequence, sRNA_length, pvalue, phase_ratio, phase_number, phase_abundance, phase_score, marker
- redundant phasiRNA cluster output
  - table header: PHAS_gene, strand, phasiRNA_position, phasiRNA_abundance, phasiRNA_record, phasiRNA_sequence, phasiRNA_length, pvalue, phase_ratio, phase_number, phase_abundance, phase_score, marker
integration module
- integrated PHAS loci information
- integration summary information
- integrated allsiRNA cluster output
  - table header: gene, strand, sRNA_position, sRNA_abundance, sRNA_record, sRNA_sequence, sRNA_length, phase_ratio, phase_number, phase_abundance, phase_score, pvalue, gene_annotation, marker
- integrated phasiRNA cluster output
  - table header: PHAS_gene, strand, phasiRNA_position, phasiRNA_abundance, phasiRNA_record, phasiRNA_sequence, phasiRNA_length, phase_ratio, phase_number, phase_abundance, phase_score, pvalue, PHAS_gene_annotation, marker
visulization module
- phasiRNA fasta file
  - id description: recorder__PHAS_gene__position__abundance__strand__order
- PHAS loci fasta file
  - id description: recorder__PHAS_gene__[start]__[end]__[extend_start]__[extend_end]__[marker]
- phasiRNA alignment result
- phasiRNA cluster plot
initiator_prediction_and_verification
- miRNA-PHAS_loci interaction output
- Predicted phase initiator output
- vertified phase initiator output with degradome data
- degradome verification t-plot
phasiRNA_target_prediction_and_verification
- phasiRNA-target interaction output
- vertified phasiRNA-target interaction with degradome data
- degradome verification t-plot

Copyright

Free for academic use. For commercial use, please contact us (huangji@njau.edu.cn)

Name		Name	Last commit message	Last commit date
Latest commit History 38 Commits
bin		bin
image		image
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
User_manual.pdf		User_manual.pdf
environment.yml		environment.yml
fasta36		fasta36
phasiHunter		phasiHunter

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