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TrueSight v0.06
2012/09/15
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Author:

Yang Li

[email protected]

Check http://bioen-compbio.bioen.illinois.edu/TrueSight/ for more details

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All pre-computed 64bit binaries are included

external programs:
"bowtie" and "bowtie-build" from:

http://bowtie-bio.sourceforge.net/index.shtml

logistic regression "train" from:

http://komarix.org/ac/lr/lrtrirls

samtools are required and should be under usr default PATH

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Run on paired-end RNA-seq data:

./truesight_pair.pl
	-p/--thread		number of cores
	-f      		[MANDATORY] input file name, fq_1 fq_2; if there are multiple files for fq_1/fq_2, they should be seperated by comma; All reads should have the same length and >= 36bp
	-r/--bowtie-index	[MANDATORY] bowtie reference dir/name, thus bowtie index should be dir/name.*.ebwt, reference genome should also be located here, e.g. dir/name.fa; chromosome line for dir/name.fa should be clean and there is no space within it, such as ">XXXXX\n"
	-v/--mismatch		mismatches (0-3)
	-s/--segment-length     segment length (18-25)
	-i/--min-intron-length
	-I/--max-intron-length
	-c/--canonical		if canonical
	-o/--output		output dir, default is truesight_out
	-h/--help	
	--segment-name


Run on single-end RNA-seq data:

./truesight_single.pl
	-p/--thread             number of cores
	-f                      [MANDATORY] input file name; if there are multiple files, they should be seperated by comma; All reads should have the same length and >= 36bp
	-r/--bowtie-index       [MANDATORY] bowtie reference dir/name, thus bowtie index should be dir/name.*.ebwt, reference genome should also be located here, e.g. dir/name.fa; chromosome line for dir/name.fa should be clean and there is no space within it, such as ">XXXXX\n"
	-v/--mismatch           mismatches (0-3)
	-s/--segment-length     segment length (18-25)
	-o/--output             output dir, default is truesight_out
	-i/--min-intron-length
	-I/--max-intron-length
	-h/--help       
	--segment-name




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Output

alignment.bam: 
	sorted bam format alignment results.

GapAli.junc:
	infered junctions

GapAli.sam:
	Gapped alignment in sam format