MicrobesInRNAseq

Find microbial sequences in human RNA sequencing data

Input:

1. krakenunique report
2. taxDB
3. cell.lines.txt

Process:

1. unique kmer filtering
2. total kmer filtering
3. study level filtering
4. correlation spearman filtering
5. cell line filtering

Output:

• /Output
  • /Study1
    • /decontamination_statistic.txt
    • /01raw_kreport
      • /sample.txt

        study	sample	rank	taxid	name	reads	totalkmer	uniq	rpm	rpmm
        PRJNA512027	SRR8378431	no rank	0	unclassified	141913	109152660.9	65754615	32290.8963486642	51717565.5976676

    • /02unique_kmer_filted
      • /sample_unique_kmer_filted.txt

        %	reads	taxReads	kmers	dup	cov	taxID	rank	taxName
        3.229	141913	141913	65754615	1.66	2453	0	no rank	unclassified

    • /03total_kmer_filted
      • /sample_total_kmer_filted.txt |study|sample|rank|taxid|name|reads|totalkmer|uniq|rpm|rpmm|unique_contamination|total_contamination|n()|sample_contamination| |-----|------|----|-----|----|-----|---------|----|---|----|--------------------|-------------------|---|--------------------| |PRJNA512027|SRR8378431|no rank|0|unclassified|141913|109152660.9|65754615|32290.8963486642|51717565.5976676|FALSE|FALSE|192|FALSE|
    • 04study_level_filted
      • sample_level_filted.txt
      • sample_level_results.txt
      • sample_study_level_filted.txt
    • 05correlation_filted
      • correlation_contamination.txt
      • correlation_filted.txt
      • correlation_summary.txt
      • sample_correlation_spearman_filted.txt
    • 06correlation_plot
    • correlation plot.pdf
    • 07cell_line_plot
    • cell line plot_genus.pdf
    • cell line plot_species.pdf
    • 08cell_line_quantative
    • cell_line_quantative.txt
    • 09sample_decontaminated_results
    • sample_filted.kreport