biocorecrg/master_of_pores

New Tombo Output

ADelgadoT opened this issue · 2 comments

ADelgadoT commented

Implement new Tombo commands to get an improved output:

Changes to process getModificationsWitTombo:

  • Modify tombo detect_modifications command:
    tombo detect_modifications level_sample_compare --fast5-basedirs ${folder_name_A}/* --alternate-fast5-basedirs ${folder_name_B}/* --statistics-file-basename ${folder_name_A}_${folder_name_B}_level_compare_sample --store-p-value

  • Delete tombo text_output signif_sequence_context command

  • Add tombo text_output browser_files command:
    tombo text_output browser_files --fast5-basedirs ${folder_name_A}/* --statistics-filename ${folder_name_A}_${folder_name_B}_level_compare_sample.tombo.stats --file-type {coverage,statistic}

Then, it will output the following files per comparison:

  • ${folder_name_A}_${folder_name_B}.coverage.sample.(plus|minus).bedgraph
  • ${folder_name_A}_${folder_name_B}.coverage.control.(plus|minus).bedgraph
  • ${folder_name_A}_${folder_name_B}.statistic.(plus|minus).wig

Adding new scripts to NanoMod/bin:

  • bedgraph2wig.pl
  • Merge_Tombo_wigs_MoP.R

New process to modify Tombo output:

  • For each bedgraph file from the previous step, run:
    perl bedgraph2wig.pl --bedgraph <infile.bedgraph> --wig <outfile.wig> --step 1 --compact

  • For each group of wig files (coverage.sample + coverage.control + statistic) per strand (plus|minus), run:
    Rscript Merge_Tombo_wigs_MoP.R -stats_wig ${folder_name_A}${folder_name_B}.statistic.(plus|minus).wig -Cov_WT ${folder_name_A}${folder_name_B}.coverage.sample.(plus|minus).wig -Cov_Control ${folder_name_A}${folder_name_B}.coverage.control.(plus|minus).wig -output ${folder_name_A}${folder_name_B}

It will output a file called: ${folder_name_A}_${folder_name_B}_Tombo_Output.tsv -> which should be placed in NanoMod's output folder.

lucacozzuto commented

Hi @ADelgadoT I miss some outputs. I sent you a DM in slack