![]() ![]() It can be downloaded from Īdd the ctk directory to your executable path: CTK: It provides a set of tools for analysis of CLIP data starting from the raw reads generated by the sequencer (Version 1.0.3,).Or you can download the index of novoalign from novoindex -k 14 -s 1 GRCH38_gencode_v23.ndx GRCh38.p3.genome.fa edit your ~/.bash_profile file to include: It can be downloaded from Īdd the novocraft directory to your executable path novoalign: It is used for mapping(V3.07.00).3 and GRCh38.p3.genome.fa: Reference genomic data (Version 23).Please refer to the "README.txt" in the homer folder for the installation method. HOMER: It is a suite of tools for Motif Discovery and next-gen sequencing analysis (Version 4.8.2).configure -prefix=$HOME -with-htslib="the path of htslib-1.9" It can be downloaded from For more information, please see SAMtools: It is a suite of programs for interacting with high-throughput sequencing data.HTSlib: A C library for reading/writing high-throughput sequencing data (Version 1.9).TopHat2: It is a fast splice junction mapper for RNA-Seq reads (Version 2.1.1,).Bowtie2: It is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.BEDTools: A powerful toolset for genome arithmetic.FASTX-Toolkit: It is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing (Version 0.0.13,).Or you can type"pip install cutadapt=1.12" to install cutadapt Cutadapt: A software for removing adapters(Version 1.12,).Type "bash run_iscancergene.sh" to to analyze the cancer information of the target protein, such as CLIP1.Īfter these step, you will get the target RBP with its interaction parter co-occour in which cancer. ![]() (3) For Clinvar, type "cd cBioPortal" to change the current directory Type "bash peak_clinvar.sh" to map the peak file to the ClinVar data to get the SNP in the peak file.Īfter these step, you will get the mutation information of the peaks. (3) For ClinVar, type "cd ClinVar" to change the current directory (2) Type "cd Clinvar_cBioPortal" to change the current directory (1) Type "tar -zxvf Clinvar_" to uncompress the package Uncompress and the usage of Clinvar_cBioPortal:ġ. If you want to use CIMS as the peak calling, please type: If you want to use Piranha as the peak calling, please type:ģ. (3) For iRIP-seq, type "bash clean_data_iRIP-seq.sh" to pre-processing the raw data įor CLIP-seq, type "bash clean_data_CLIP-seq.sh" to pre-processing the raw data.Īfter these step, you will get the cleaned data.Ģ. (2) Type "cd phdRBP" to change the current directory ![]() (1) Type "tar -zxvf " to uncompress the package Raw data or peak files can be downloaded from:.PhdRBP ( Pipline for High-throughput Data analysis for RNA- Binding Protein) is available: ![]()
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