rscs's Introduction

RSCS

Here, we developed a computational pipeline that integrates RNA-seq and small RNA-seq data, denoted RSCS, and this strategy greatly improves the resolution and accuracy of transcriptome annotation in a wide variety of mammalian samples.

Install

To install RSCS, be sure to have the appropriate rights and run :

  tar -zxvf v1.1.0.tar.gz
  cd RSCS-1.1.0
  make

Example

Here is the help message:

  Description: RSCS:RNA-seq and small RNA-seq combined strategy,
                    a newly cpmputational pipeline to predict mouse transcripts.

  usage: RSCS <ARGUMENTS> [OPTIONS]

  ARGUMENTS:
          -r --rnaseq_dir          RNA-seq dirctory,file format in this dirctory
          -s --srnaseq_dir         Small RNA-seq dirctory,file format in this dirctory
          -e --reference           The basename of the index for the reference genome. The basename is the name of any of the
                                   index files up to but not including the final .1.ht2 / etc. hisat2 looks for the specified
                                   index first in the current directory, then in the directory specified in the HISAT2_INDEX
                                   environment variable
          --single_or_pairedr      Logical value of RNA-seq[TRUE or FALSE]
          --single_or_paireds      Logical value of Small RNA-seq[TRUE or FALSE]
          -m --meta_data           Merge bam meta-data file,which is tab separate. file format:
                                                                                                  sample1         sample2
                                                                                                  SRR2089677      SRR1200367
                                                                                                  SRR1005345      SRR1234123
          -o --outputdir           Output dirctory
  OPTIONS:
          -h --help                Show this message
          -p --threads INT         Number of input/output compression threads to use in addition to main thread. Default[1]
          -k --kmer INT            It searches for at most <int> distinct, primary alignments for each read. Default[5]
          -v --version             show version

Please see the example folder for the specific RSCS example.

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