Table 8-1 summarizes the BLAT options.
Table 8-1. BLAT options
| Option | Definition | Default |
| -dots=N | Output dot every N sequences to show the program's progress. | |
| -makeOoc=N.ooc | Make overused tile file. | |
| -mask=type | Mask out repeats. Alignments won't be started in masked region but may extend through it in nucleotide searches. Masked areas are ignored entirely in protein or translated searches. Types are: lower = Mask out lowercased sequence. upper = Mask out uppercased sequence. out = Mask according to database.out RepeatMasker .out file. file.out = Mask database according to RepeatMasker file.out. | |
| -maxGap=N | Sets the size of maximum gap between tiles in a clump. Usually set from 0 to 3. Only relevant for minMatch > 1. | 2 |
| -minIdentity=N | Sets minimum sequence identity (in percent). | 90 (nucleotide) 25 (protein) 25 (translated) |
| -minMatch=N | Sets the number of tile matches. Usually set from 2 to 4. | 2 (nucleotide) 1 (protein) |
| -minScore=N | Sets minimum score. This is twice the matches minus the mismatches minus some sort of gap penalty. | 30 |
| -minRepDivergence=NN | Minimum percent divergence of repeats to allow them to be unmasked. Only relevant for masking using RepeatMasker .out files. | 15 |
| -noHead | Suppress .psl header (so it's just a tab-separated file). | |
| -noTrimA | Don't trim trailing poly-A. | |
| -oneOff=N | If set to 1, this allows one mismatch in tile and still triggers an alignment. | 0 |
| -ooc=N.ooc | Use overused tile file N.ooc. N should correspond to the tileSize. | |
| -out=type | Controls output file format. Type is one of: psl = Tab-separated format without actual sequence. pslx = Tab-separated format with sequence. axt = blastz-associated axt format. maf = multiz-associated maf format. wublast = similar to wublast format. blast = similar to NCBI blast format. | psl |
| -prot | Synonymous to -d=prot -q=prot. | |
| -qMask=type | Mask out repeats in query sequence. Similar to -mask, but for query rather than target sequences. | |
| -q=type | Query type. Type is one of: dna = DNA sequence. rna = RNA sequence. prot = protein sequence. dnax = DNA sequence translated in six frames to protein. rnax = DNA sequence translated in three frames to protein. | dna |
| -repMatch=N | Sets the number of repetitions of a tile allowed before it is marked as overused. Typically this is: 256 for tileSize 12. 1024 for tile size 11. 4096 for tile size 10. Typically comes into play only with makeOoc. | 1024 |
| -t=type | Database type. Type is one of: dna = DNA sequence. prot = protein sequence. dnax = DNA sequence translated in six frames to protein. | dna |
| -tileSize=N | Sets the size of match that triggers an alignment. Usually between 8 and 12. | 11 (DNA) 5 (protein) |
| -trimHardA | Removes poly-A tail from qSize and alignments in psl output. | |
| -trimT | Trims leading poly-T. | |
