Quiclick is a python package provides analysis tools for RNA-seq and RNA editing analysis. We recommand exectue the files in an anaconda environment with python 3.x.
Due to some reasons from author, this project will no longer upgrade. Check our paper in RNA editing
Enter the following command in your terminal, then you can use command "quiclick" directly(NOT recommand). Because of the network of sourceforge, a Tsinghua cloud link is also provided: https://cloud.tsinghua.edu.cn/f/c77843c493e64a2a9602/, one can download a compressed package.
wget https://sourceforge.net/projects/quiclickrnaseq/files/quiclick.tar.gz
tar zxvf quiclick.tar.gzThen use binary command to test whether the package is installed:
[username@localhost filename]python <quiclickPath>/quiclick/bin/quiclick.py
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Users help documentation
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Parameters Description Default & Note Optional(Y/N)
-w Pathway of raw data Current path Y
-i Pathway of index files Create automatically (ENSEMBL version) Y
-m Multiprocessing for mapping Single thread (supported files < 6) Y
-p Threads for mapping 16 (CANNOT use with -m altogether) Y
-E RNA editing analysis model Carry out RNA editing analysis Y
-D Whether to execute differential expression analysis NO Y
-k Whether to save genome index files Do not save Y
-s Species N/A (necessary parameter) N
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-w:
The ABSOLUTE PATH of raw data, if not, the path will be set as current data. And the raw data file must be listed as the structure showed below:
rawdata/
├── a1
│ ├── a1_1.fq.gz
│ ├── a1_2.fq.gz
├── a2
│ ├── a2_1.fq.gz
│ ├── a2_2.fq.gz
├── b1
│ ├── b1_1.fq.gz
│ ├── b2_2.fq.gz
├── b2
│ ├── b2_1.fq.gz
│ ├── b2_2.fq.gz
|___-i:
The ABSOLUTE PATH of index file, and must be indexed by STAR, what's more, fasta and gtf files need to be saved in the same directory.
-m:
If -m is set, mapping process will be exectued in a multi-processing way, not supported when sample numbers > 6.
-p:
If not must-processing for mapping , you can set a thread number for your mapping processing, 20-50 is recommended.
-E:
If -E is set, RNA editing process will be executed.
-D:
If -D is set, differential expression analysis will be execute, note that you need to point out experimental samples and control samples, and the number of each group MUST >=2.
-k:
if -k is set, index files will be save in your work path with name "refs", you can keep it for your next time's analysis.
-s:
-s is the only nessary parameter to point out which species you want to analysis, only support human, mouse, zebrafish and C. elegans.
Useage example of quiclick:
python quiclick.py -w /home/Andrew/rawdata/ -i /home/Andrew/index/ -s celegans -m -E -D -kWhat's more, we here describe the usage of pyRED. pyRED is a python file including two functions for analytics of differential RNA editing sites and the co-variaty of RNA edting with certain variable, whose outputs are p-value and slope of the linear regression respectively. The detailed description of function is written in the functions' description.
from pyRED import differentialEditingSiteEstimation
exprEditList = [1,1]
exprTotalList = [19,20]
ctrlEditList = [9,10]
ctrlEditList = [11，11]
EDTI = [1,1,9,10]
TOTAl = [19,20,11,11]
pValueOfExprToCtrlSample = differentialEditingSiteEstimation(exprEditList, exprTotalList, ctrlEditList, ctrlEditList, EDIT, TOTAL)
from pyRED import editingCovarEstimation
editCounts = [1,1,10]
totalCounts = [11,12,11]
covarsList = [1,2,3]
pValueOfCovars, slpoeOfCovars = editingCovarEstimation(editCounts, totalCounts, co)Output file structure will contain several new directories:
refs: containing index file generated by STAR.
trimmed_data: containing RNA-seq data formatted as .fq.gz, which is trimmed by trim_galore.
mapping_output: containing BAM file generated by STAR.
RES_res: containg RNA editing results.
.count files: generated by htseq-count, indicating the reads counts from each sample.
Differential_Express_analysis.R: used for differential expression analysis, the output will be saved in current path.
NOTE: File Differential_Express_analysis.R is used for differential expression analysis, exectue Rscript Differential_Express_analysis.R to get the ouput table and plots. And package DESeq2 and gglot2 need to be installed in advance. Meanwhile, binary file of quiclick is no longer provided, pandas,numpy,matplotlib pacakages need to be installed in your environment.
rawdata/
├── a1
│ ├── a1_1.fq.gz
│ ├── a1_2.fq.gz
│ ├── mappingProcess.log
│ ├── RES_res
│ │ ├── Gene_edit_count.txt
│ │ ├── PARAMETER.txt
│ │ ├── SPRINT_gene_annotation.res
│ │ ├── SPRINT_identified_all.res
│ │ ├── SPRINT_identified_hyper.res
│ │ ├── SPRINT_identified_regular.res
| | └── tmp
│ └── trimmed_data
│ ├── a1_1.fq.gz_trimming_report.txt
│ ├── a1_1_val_1.fq
│ ├── a1_1_val_1.fq.gz
│ ├── a1_2.fq.gz_trimming_report.txt
│ ├── a1_2_val_2.fq
│ ├── a1_2_val_2.fq.gz
│ └── editingProcess.log
├── DESeq2_res_order.txt
├── Differential_Express_analysis.R
├── Expressed_genes.txt
├── refs
└── Rplots.pdf2020/9/27
Binary file of quiclick is no longer provided.
Added script: pyRED for RNA editing differential analysis.
Contact: [email protected] when questions arise.