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4.5.5 Merge density

Function

Single-sample density files generated by rna_Density or rpf_Density must be merged before most multi-sample downstream analyses.

This page documents two commands:

  1. merge_dst_list: build the sample list required by rpf_Merge.
  2. rpf_Merge: merge all density files listed in the sample list into one matrix-like file.

merge_dst_list

Function

merge_dst_list creates a three-column sample list containing sample name, density file path, and density type.

Input files

Input Description
Density files Single-sample *_rpf.txt or *_rna.txt files. File names must end with _rpf.txt or _rna.txt so the command can infer the sample type.

Parameters

Parameter Required Description
-l / --list Yes Input density files. Multiple files can be provided.
-o No Output sample list file. If omitted, the command writes RPF.file.list for Ribo-seq input or RNA.file.list for RNA-seq input.

Output files

Output Description
RPF.file.list or RNA.file.list Default output sample list file when -o is not provided.
User-defined list file Output sample list file when -o is provided.

Example

merge_dst_list \
    -l ../04.density/*_rpf.txt \
    -o RIBO.file.list

merge_dst_list \
    -l ../04.density/*_rna.txt \
    -o RNA.file.list

Sample list format

Name    File    Type
sample1 /path/to/sample1_rpf.txt    Ribo
sample2 /path/to/sample2_rpf.txt    Ribo

rpf_Merge

Function

rpf_Merge merges single-sample density files into a multi-sample density matrix. The merged file is used by periodicity, metaplot, coverage, correlation, gene-level, codon-level, and smORF modules.

Input files

Input Description
Density list Sample list generated by merge_dst_list.

Parameters

Parameter Required Description
-l Yes Input sample list file in TXT/TSV format.
-o Yes Output prefix. The output file is <prefix>_merged.txt.

Output files

Output Description
<prefix>_merged.txt Merged RNA-seq or Ribo-seq density matrix.
<prefix>.log Running log if redirected by the user.

Example

rpf_Merge \
    -l RIBO.file.list \
    -o RIBO \
    &> RIBO.log

rpf_Merge \
    -l RNA.file.list \
    -o RNA \
    &> RNA.log

Notes

  • Check that sample names in the list file are unique.
  • The merged output file is always named <prefix>_merged.txt.
  • rpf_Merge removes rows whose codon column contains N.