Table 8-1. BLAT options
|
-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.
|
|
