The RF RCTools module enables easy visualization/manipulation of RC files. It allows indexing, merging and dumping RC files.
This tool is particularly useful when the same sample is sequenced more than one time to increase its coverage. Now, instead of merging the BAM files and re-calling the rf-count on the whole dataset (that is very time-consuming), each sample can be processed independently and simply merged to the RC file from the previous analysis.

Usage

To list the required parameters, simply type:

$ rf-rctools [tool] -h

Available tools are: index, view and merge

Parameter Tool Type Description
-t or --tab view Switches to tabular output format
-o or --output merge string Output RC filename (Default: merge.rc)
-ow or --overwrite merge Overwrites output file (if the specified file already exists)
-i or __--index_ merge string[,string] A comma separated (no spaces) list of RCI index files for the provided RC files
Note: RCI files must be provided in the same order as RC files. If a single RCI file is specified along with multiple RC files, it will be used for all of them.
-T or --tmp-dir merge string Temporary directory (Default: /tmp)

## RCTools "view" output
By default, the view command produces an output structured as follows:
Transcript_1
ATGGGCAGCTATGCA...TGGGCATGCTGGATG
0,0,0,3,1,2,5,9,16,26,10,14,21,899,888,1038,112,96,1135,167,1164,139,161,3520,2522,2075,172,2043,185,205
245496,239926,233144,232804,232485,229422,225754,224062,222318,219039,216337,212885,207928,206206,203534,184536,184118,185854,183831,180871,177687,174523,170546,167506,163845,161977,150523,150637,143787,142784,137815

Transcript_2
GAATTCATGCATGCG...AGCTAGCGGGGATAT
0,0,0,1,0,2,5,30,17,17,15,34,46,32,409,48,509,56,480,499,68,715,677,782,74,1016,988,2035,108,158
512,583,702,783,847,1517,1852,2084,2191,4791,10389,15321,16535,17231,17823,18254,19388,22321,22944,25503,27254,28285,36273,41905,50366,50724,71321,73144,77610,77903

Transcript_n
ATTGCTTCCAATGAA...AATATGGAGACTATG
150,2152,161,3557,3109,137,3077,190,157,3105,3923,3047,3199,158,2931,159,3501,149,3938,159,162,159,177,186,5684,281,4734,3800,6114,4736
504075,499650,493631,489064,480388,478484,477320,468301,462674,457668,438438,428879,418411,411484,404875,404148,403917,402996,409478,408878,398653,394306,390252,370852,360041,361397,359538,359530,359542,363686

in which each transcript is reported as a 4-rows entry, with rows ordered as follows:

  • Transcript ID
  • Transcript sequence
  • Number of per-base RT-stops (or mutations)
  • Per-base coverage

When the -t parameter is specified, the output is instead structured as follows:

Transcript_1
A       0       242
G       0       280
C       0       359
G       3       390
...
A       1038    56642
T       112     65943
T       96      66134
A       1135    74888

Transcript_2
T       185     100294
G       205     100831
G       185     101003
A       1458    101124
...
A       2529    101509
A       2984    101819
G       227     103858
A       2937    105307

Transcript_n
C       0       945
G       13      990
A       3       1064
A       5       1893
...
A       3       2333
G       36      2648
C       25      2993
A       30      14274

in which each transcript is reported as a multi-row entry (with the number of rows equal to transcript's length). Each row is made of 3 tab-spaced fields, ordered as follows:

  • Base
  • Number of RT-stops (or mutations)
  • Coverage

Consecutive entries are separated by a newline.