NanoMod

This module allows to predict the loci with RNA modifications starting from data produced by NanoPreprocess.

Workflow

  • index_reference index the reference file for Epinano
  • call_variants uses Samtools for calling the variants for Epinano
  • calc_var_frequencies it uses TSV_to_Variants_Freq.py3 for calculating the frequencies of each variants for Epinano
  • predict_with_EPInano It predicts the modifications with Epinano in parallel splitting the input file in 1 million rows
  • combineEpinanoPred It combine the results from Epinano
  • resquiggling resquiggle fast5 files for Tombo
  • getModifications it estimates the modifications using Tombo comparing WT vs KO

Input Parameters

  1. input_path path to the folders produced by NanoPreprocessing step.
  2. comparison tab separated text file containing the list of comparison. Here an example: 
    WT1 KO1
WT2 KO2
WT3 KO3
  3. reference reference transcriptome
  4. output folder
  5. coverage read coverage threshold for prediction
  6. tombo_opt options for tombo
  7. epinano_opt options for epinano
  8. email

Results

Three folders are produced by this module:

  1. Epinano, containing the results obtained with this method. You have a single file with putative modifications.
#Kmer,Window,Ref,Coverage,q1,q2,q3,q4,q5,mis1,mis2,mis3,mis4,mis5,ins1,ins2,ins3,ins4,ins5,del1,del2,del3,del4,del5,prediction,dist,ProbM,Pro
bU
AGTGG,394404:394405:394406:394407:394408,chr2,8.0:8.0:7.0:7.0:7.0,21.5,21.25,19.857,23.0,16.285999999999998,0.0,0.0,0.0,0.0,0.0,0.0,0.062,0.0
71,0.0,0.0,0.0,0.0,0.0,0.0,0.0,unm,19.26143361547619,3.00000089999998e-14,0.9999999999999699
TTTTT,12150:12151:12152:12153:12154,chr8,3.0:3.0:3.0:3.0:3.0,0.0,16.5,18.5,16.0,16.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,1.0,0.3329999999
9999996,0.33299999999999996,0.0,0.0,unm,2.5976484688977424,0.06071658133381308,0.9392834186661868
ACATT,438165:438166:438167:438168:438169,chr13,67.0:67.0:67.0:68.0:68.0,13.635,13.446,9.323,9.6,12.127,0.03,0.045,0.015,0.147,0.0740000000000
0001,0.0,0.0,0.0,0.0,0.0,0.06,0.03,0.075,0.11800000000000001,0.07400000000000001,unm,0.08435556637195174,0.519879422458087,0.4801205775419129
5...
  1. Tombo, containing the results obtained with this method in fasta format. You have one file for each comparison WT vs KO
>chr11:455562:- Est. Frac. Alternate: 0.98
TGACA
>chr12:1008723:- Est. Frac. Alternate: 0.98
TATCT
>chr15:491587:+ Est. Frac. Alternate: 0.96
TATAT
>chr10:425794:- Est. Frac. Alternate: 0.95
ATGTT
>chr13:510759:+ Est. Frac. Alternate: 0.95
...