Category

Generic


Usage

creates: <outFilePrefix>.pairs file


Manual

This tool is part of UCSC Genome Browser's utilities.

pslFile - filtered psl alignments of ends from kluster run
pairFile - three column tab separated: forward reverse cloneId
- forward and reverse columns can be comma separated end ids
pslTableName - table name the psl alignments have been loaded into
outFilePrefix - prefix used for each output file name
Options:
-max=N - maximum length of clone sequence (default=47000)
-min=N - minimum length of clone sequence (default=32000)
-slopval=N - deviation from max/min clone lengths allowed for slop report
- (default=5000)
-nearTop=N - maximium deviation from best match allowed (default=0.001)
-minId=N - minimum pct ID of at least one end (default=0.96)
-minOrphanId=N - minimum pct ID for orphan alignment (default=0.96)
-tInsert=N - maximum insert bases allowed in sequence alignment
- (default=500)
-hardMax=N - absolute maximum clone length for long report (default=75000)
-verbose - display all informational messages
-noBin - do not include bin column in output file
-noRandom - do not include placements on random portions
- {length(chr name) < 7}
-slop - create .slop file of pairs that fall within
- slop length
-short - create .short file of pairs shorter than
- min size
-long - create .long file of pairs longer than
- max size, but less than hardMax size
-mismatch - create .mismatch file of pairs with
- bad orientation of ends
-orphan - create .orphan file of unmatched end sequences


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