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.
To list the required parameters, simply type:
$ rf-rctools [tool] -h
Available tools are: index, view and merge
|-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
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
-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:
- Number of RT-stops (or mutations)
Consecutive entries are separated by a newline.