Manual

Name

CLIIQ - tool for simultaneously identify and quantify of expressed isoforms in a population

DESCRIPTION

Requirement
  • POSIX compatible system
  • IBM ILOG CPLEX Optimizer
Mandatory Parameters

-g, --gtf
Specify the gene annotation file name. The gtf file should follow ensembl specifications, and contain correct gene_id entry.

-s, --sam
Specify the SAM file name. It should contain the mapping results against reference genome, and sorted by coordinate. If no file is specified, standard input will be used.
Utility Parameters

-h, --help
Prints short usage information.

-v, --version
Prints the current version of CLIIQ.
Modeling Parameters

-m, --mode
Specify the model in determining isoform candidates (Default value 1).

  • 1: consider all possible isoforms
    • In mode 1, CLIIQ will consider all possible isoforms (including all possible novel junctions) based on known exonic boundaries. For example, if a gene contains one known isoform A-B-C in which A, B, C are exons. CLIIQ in mode 1 will consider 7 possible isoforms based on these exons.
  • 2: preference mode: it works like mode 1, but favors known isoforms
    • In mode 2, CLIIQ will consider all possible isoforms as in mode 1, but favor known isoforms when there are multiple feasible solutions.
  • 3: consider only known isoforms
    • In mode 3, CLIIQ will consider ONLY known isoforms. The behaviour will be similar to the quantification tools IsoEM or RSEM.

-o, --output
Specify the name of output folder containing resultant gtf files (Default value is ./temp/).
CLIIQ will create this folder (if it does not exist) and write resultant files in it.

-e, --error
Specify the error tolerance used in modeling ILP, the integer linear program, of CLIIQ (Default value 0.4).
Conceptually it stands for the relative error tolerance between estimated expression values and real mapping results. Caution: smaller values might lead to infeasible solutions in ILP modeling.

-b, --buffer
Specify the pre-allocate buffer size in processing SAM file (Default value 1000000).
CLIIQ will keep these number of reads in memory. Higher values lead to better efficiency, and take larger virtual memory. The default values can take 12 GB of virtual memory in running.
Decrease this value if you have memory issues.

-d, --verbose
Specify the verbose mode from 0 to 5 (Default value 0).
Higher values output more information.

Example Usage

/home/mycode/cliiq-0.1.0.1/cliiq -m 1 -g gene.gtf -s mapping.sam -e 0.2 -o ./output/ -b 100000 -d 2
CLIIQ runs in mode 1 (consider all possible isoforms), build ILP in which quantification error tolerances is 0.2 (20%), and pre-allocate a buffer capable of storing 100000 strings in processing SAM file. The resuls are written into the folder ./output/.

/home/mycode/cliiq-0.1.0.1/cliiq -m 2 -g gene.gtf -s mapping.sam -e 0.3 -o ./output/ -b 500000 -d 5
CLIIQ runs in mode 2 (consider all possible isoforms but favor known ones), build ILP in which quantification error tolerances is 0.3 (30%), and pre-allocate a buffer capable of storing 500000 strings in processing SAM file. The resuls are written into the folder ./output/.
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