Is your query sequence an unusual size ?
To run per-chrom:
$ twoBitInfo hg18.2bit stdout | cut -f1 | while read C
do
blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 -out=blast9 \
hg18.2bit:${C} test_seq.txt test_seq_blas9.${C}.out
done
If you use the default output format of PSL you could then use the various
psl* commands to filter the output.
--Hiram
Vinodh Srinivasasainagendra wrote:
> Mine looks like:
>
> core file size (blocks, -c) 0
> data seg size (kbytes, -d) unlimited
> scheduling priority (-e) 0
> file size (blocks, -f) unlimited
> pending signals (-i) 139264
> max locked memory (kbytes, -l) 32
> max memory size (kbytes, -m) unlimited
> open files (-n) 1024
> pipe size (512 bytes, -p) 8
> POSIX message queues (bytes, -q) 819200
> real-time priority (-r) 0
> stack size (kbytes, -s) 10240
> cpu time (seconds, -t) unlimited
> max user processes (-u) 139264
> virtual memory (kbytes, -v) unlimited
> file locks (-x) unlimited
>
>
> Which of the above parameters should I bump up?
>
> How to run blat per chromosome basis?
>
> thanks
> vinodh
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