Category
Generic
Usage
mrnaToGene [options] psl genePredFile
Manual
This tool is part of UCSC Genome Browser's utilities.
Convert PSL alignments with CDS annotation from genbank to gene
annotations in genePred format. Accessions without valids CDS are
optionally dropped. A best attempt is made to convert incomplete CDS
annotations.
The psl argument may either be a PSL file or a table in a databases,
depending on options. CDS maybe obtained from the database or file.
Accession in PSL files are tried with and with out genbank versions.
Options:
-db=db - get PSLs and CDS from this database, psl specifies the table.
-cdsDb=db - get CDS from this database, psl is a file.
-cdsFile=file - get CDS from this database, psl is a file.
File is table seperate with accession as the first column and
CDS the second
-insertMergeSize=8 - Merge inserts (gaps) no larger than this many bases.
A negative size disables merging of blocks. This differs from specifying zero
in that adjacent blocks will not be merged, allowing tracking of frame for
each block. Defaults to 8 unless -cdsMergeSize or -utrMergeSize are specified,
if either of these are specified, this option is ignored.
-smallInsertSize=n - alias for -insertMergetSize
-cdsMergeSize=-1 - merge gaps in CDS no larger than this size.
A negative values disables.
-cdsMergeMod3 - only merge CDS gaps if they mod 3
-utrMergeSize=-1 - merge gaps in UTR no larger than this size.
A negative values disables.
-requireUtr - Drop sequences that don't have both 5' and 3' UTR annotated.
-genePredExt - create a extended genePred, including frame information.
-allCds - consider PSL to be all CDS.
-noCds - consider PSL to not contain any CDS.
-keepInvalid - Keep sequences with invalid CDS.
-quiet - Don't print print info about dropped sequences.
-ignoreUniqSuffix - ignore all characters after last `-' in qName
when looking up CDS. Used when a suffix has been added to make qName
unique. It is not removed from the name in the genePred.
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