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## TranspoSeq v1.0
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## Elena Helman
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## September 29, 2012
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Make sure 
## use R-2.10
## use LSF
## use BLAST

## TranspoSeq takes in 
"tumorbam": Path to tumor BAM file, filename must not contain any internal
periods
"normalbam": Path to normal BAM file, filename must not contain any internal
periods
"tumorname": Tumor type name
"samplename": Name of sample
"hgnum": Genome reference BAM files are aligned to, for example, "18"
"dir": Directory where folders will be created
"readsfold": Directory where files with reads will be written
"nalign": Minimum alignment parameter for BLAST - number of aligned bp necessary to count as 'aligned' to db, e.g., 27
"percentident": Minimum percent identity parameter for BLAST, e.g., 90
"nreads": Minimum reads necessary to support candidate event
"fasta": Name of retrotransposon db, e.g., "L1s"
"fastafile": File path to retrotransposon db fastafile, e.g., "/home/L1s.fasta"
"queue": LSF queue to send jobs to

## To run
RUN_TRANSPOSEQ.sh tumorbam normalbam tumorname samplename hgnum dir readsfold nalign percentident fasta fastafile queue &
